Psyllid ID: psy8714

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560--
Protein Sequence
MHLRVKKLVPASEIKLARPSLISLLTPLQRMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPTEKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVGDHPPITPTKLATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRVQA
Secondary Structure (PSIPRED)
ccccccEEEEEcccccHHHHHHHHHcccccccccEEEEEEccccccccEEEEEEEEcccccccccccccccccccccccccccccEEEEccccccHHHHHHHHHccccEEEEEccccHHHHHHHHHHHHHHHHHHccccccEEEEEEEccccHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHccccHHHHHHHcccccccccccEEcccccHHHHHHHHHHHHHHHcccccccEEEEEEEEEccEEEEEEEcccccccHHHHHHHHHHHHccccEEEEEEEEEEccccccccccHHHHHHHHHHHccccHHHHHHHHHHHHHcccccccccccccccccccHHHHHHHHHccccHHHHHHHHHHccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHcccccEEEEEEEEEEEccEEEEEEEEEEEEccccccccccccccccccccccccEEEccEEEcccccccccccccHHHHHHHHHHccccccccHHHHHHHHHcccEEEEccccEEEccHHHHHHHHHHHHcccccccHHHHHHHHHHc
Secondary Structure Prediction (SSPRO)
ccccHEEEEEEccHHHHHHHHHHHHHHHccHHcccEHHHHccccccccEEEEEEEEEcEEEccccccccccccccccccccccccEEEEcccccHHHHHHHHHHHcccEEEEEcccccHHHHHHHHHHHHHcccccccccccEEEEEEcHccHHHHHHHHHccccccHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHcccHHHcccccccccHHHHHHHEHHHHHHHHccccHEEEEEEEEcccccEEEEEEEccccccHHHHHHHHHHHHccccEEEEEEEcccccccccccccHHHHHHHHHHHccccHHHHHHHHHHHHHcccEEEcccccccccHHHHHHHHHHHHHHHHccHHHcccccccccccccccccccccccccccccccHHHccHHHHHHHHHHHHHHHHHcccccEEEEEEEEEEEccEEEEEEcEEEEccccEEEEcccccccccccccccccEEEEEEEccccccccccccccHHHHHHHHHHccccccccHHHHHHHHHHccEEEEEcccEEcccHHHHHHHHHHHHHcHHHccccHHHHHHHcc
Coil and Loop (DISEMBL)
mhlrvkklvpaseiklarpslislltplqrmngacsvhewvgplfGDLVLFKMTSVCghimgldftskynnwdkvdplelfscptekreatpklklpaflaneaKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNLVkpnifearsvdARQELDLRIGCAFTRYQTKffqgkygdldaslisygpcqtptlgfcverhdkirtfkpepywlldlTLNLNGVAVSVtwsrghifdkstCNVFFKAVEKEKHVTVVDVqsstksktkpqalNTVELMRVAssglgmgphhAMQIAERLYTqgyvsyprtettqypenFDLVAVLRQqesspdwgDHVREVLSngiskprkgkdvgdhppitptklatrtqldgdAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYllhpgftgvMTWSamknesipdfkpgdlipiqsvkmverkttppdylteSELISLMEkhgigtdasipvhinnicqrnyvtvtsgrrlvptSLGIVLVHGYQKIDRELVEPTMRSAYRVQA
Flexible Loop (DISEMBL)
mhlrvkklvpaseiklarpslISLLTPLQRMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPTEKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRhqininspktVWRARFSAITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVtvvdvqsstksktkpqalnTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENFDLVAVLRQQesspdwgdHVREVLSngiskprkgkdvgdhppitptklatrtqldGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLvhgyqkidrelveptmrsayrvqa
Low Complexity Region (SEG)
MHLRVKKLVPASEIKLARPSLISLLTPLQRMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPTEKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVGDHPPITPTKLATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRVQA
Disordered region (IsUnstruct)
************EIKLARPSLISLLTPLQRMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPTEKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDV*****************LMRV***GLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENFDLVAVLR****************************************ATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKMV*******DYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELV************
Disordered Region (DISOPRED)
**LRVKKLVPASEIKLARPSLIS**********ACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPTEKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVT****************LNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHV*******************HPPITPTKLAT****DGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVK*****TTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRVQ*
Disordered Region (DISEMBL)
MHLRVKKLVPASEIKLARPSLISLLTPLQRMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPTEKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHV*************KPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVGDHPPITPTKLATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRVQA
Disordered Region (DISPRO)
**LRVKKLVPASEIKLARPSLISLLTPLQRMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPTEKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVL******************ITPTKLATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRV**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MHLRVKKLVPASEIKLARPSLISLLTPLQRMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPTEKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVGDHPPITPTKLATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRVQA
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	562	2.2.26 [Sep-21-2011]
O95985	862	DNA topoisomerase 3-beta-	yes	N/A	0.955	0.622	0.627	0.0
Q9Z321	862	DNA topoisomerase 3-beta-	yes	N/A	0.944	0.616	0.626	0.0
O96651	875	DNA topoisomerase 3-beta	yes	N/A	0.923	0.593	0.629	0.0
O70157	1003	DNA topoisomerase 3-alpha	no	N/A	0.973	0.545	0.389	1e-106
Q13472	1001	DNA topoisomerase 3-alpha	no	N/A	0.980	0.550	0.386	1e-105
O61660	759	DNA topoisomerase 3 OS=Ca	no	N/A	0.911	0.674	0.374	1e-100
Q9NG98	1250	DNA topoisomerase 3-alpha	no	N/A	0.916	0.412	0.367	8e-95
Q8T2T7	828	DNA topoisomerase 3 OS=Di	yes	N/A	0.886	0.601	0.350	1e-91
O60126	622	DNA topoisomerase 3 OS=Sc	yes	N/A	0.900	0.813	0.325	3e-79
P13099	656	DNA topoisomerase 3 OS=Sa	yes	N/A	0.882	0.756	0.325	1e-75

>sp|O95985|TOP3B_HUMAN DNA topoisomerase 3-beta-1 OS=Homo sapiens GN=TOP3B PE=1 SV=1

 Score =  700 bits (1807), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 340/542 (62%), Positives = 403/542 (74%), Gaps = 5/542 (0%)

Query: 25  LTPLQRMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFS-C 83
           L+  + +NGACSVHE+ G   G  V FKMTSVCGH+M LDF  KYN WDKVDP ELFS  
Sbjct: 26  LSSHKGLNGACSVHEYTGTFAGQPVRFKMTSVCGHVMTLDFLGKYNKWDKVDPAELFSQA 85

Query: 84  PTEKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQINI--NSPK 141
           PTEK+EA PKL +  FL  E + C+++VLWLDCDKEGENICFEV++AV   +N      K
Sbjct: 86  PTEKKEANPKLNMVKFLQVEGRGCDYIVLWLDCDKEGENICFEVLDAVLPVMNKAHGGEK 145

Query: 142 TVWRARFSAITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYG 201
           TV+RARFS+ITD DI  AM  L +P+  EA SVDARQELDLRIGCAFTR+QTK+FQGKYG
Sbjct: 146 TVFRARFSSITDTDICNAMACLGEPDHNEALSVDARQELDLRIGCAFTRFQTKYFQGKYG 205

Query: 202 DLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLN-GVAVSVTWSRGHIF 260
           DLD+SLIS+GPCQTPTLGFCVERHDKI++FKPE YW+L   +N +   ++ + W R  +F
Sbjct: 206 DLDSSLISFGPCQTPTLGFCVERHDKIQSFKPETYWVLQAKVNTDKDRSLLLDWDRVRVF 265

Query: 261 DKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIA 320
           D+    +F    + EK   V       K+K +P ALNTVE++RVASS LGMGP HAMQ A
Sbjct: 266 DREIAQMFLNMTKLEKEAQVEATSRKEKAKQRPLALNTVEMLRVASSSLGMGPQHAMQTA 325

Query: 321 ERLYTQGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVG 380
           ERLYTQGY+SYPRTETT YPENFDL   LRQQ + P W D V+ +L+ GI++PRKG D G
Sbjct: 326 ERLYTQGYISYPRTETTHYPENFDLKGSLRQQANHPYWADTVKRLLAEGINRPRKGHDAG 385

Query: 381 DHPPITPTKLATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAK 440
           DHPPITP K AT  +L GDAWRLY+YI RHFI T+  D  Y Q    F +  E+FT   K
Sbjct: 386 DHPPITPMKSATEAELGGDAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPELFTCSGK 445

Query: 441 YLLHPGFTGVMTWSAMK-NESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEK 499
            +L PGFT VM W ++   ES+P  + GD  P+  VKM+E++T PPDYLTE+ELI+LMEK
Sbjct: 446 TVLSPGFTEVMPWQSVPLEESLPTCQRGDAFPVGEVKMLEKQTNPPDYLTEAELITLMEK 505

Query: 500 HGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYR 559
           HGIGTDASIPVHINNICQRNYVTV SGRRL PT+LGIVLVHGY KID ELV PT+RSA  
Sbjct: 506 HGIGTDASIPVHINNICQRNYVTVESGRRLKPTNLGIVLVHGYYKIDAELVLPTIRSAVE 565

Query: 560 VQ 561
            Q
Sbjct: 566 KQ 567

Releases the supercoiling and torsional tension of DNA introduced during the DNA replication and transcription by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand than undergoes passage around the unbroken strand thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone (By similarity). Possesses negatively supercoiled DNA relaxing activity.
Homo sapiens (taxid: 9606)
EC: 5EC: .EC: 9EC: 9EC: .EC: 1EC: .EC: 2

>sp|Q9Z321|TOP3B_MOUSE DNA topoisomerase 3-beta-1 OS=Mus musculus GN=Top3b PE=2 SV=1

 Score =  693 bits (1788), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 336/536 (62%), Positives = 401/536 (74%), Gaps = 5/536 (0%)

Query: 31  MNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFS-CPTEKRE 89
           +NGACSVH++ G   G  V FKMTSVCGH+M LDF  KYN WDKVDP ELFS  PTEK+E
Sbjct: 32  LNGACSVHKYTGTFAGQPVHFKMTSVCGHVMTLDFLGKYNKWDKVDPAELFSQAPTEKKE 91

Query: 90  ATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQINI--NSPKTVWRAR 147
           A PKL +  FL  E + C+++VLWLDCDKEGENICFEV++AV   +N   N  KTV+RAR
Sbjct: 92  ANPKLNMVKFLQVEGRGCDYVVLWLDCDKEGENICFEVLDAVLPVMNNAHNGEKTVFRAR 151

Query: 148 FSAITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASL 207
           FS+ITD DI  AM  L +P+  EA SVDARQELDLRIGCAFTR+QTK+FQGKYGDLD+SL
Sbjct: 152 FSSITDTDICNAMTRLSEPDHNEALSVDARQELDLRIGCAFTRFQTKYFQGKYGDLDSSL 211

Query: 208 ISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNGV-AVSVTWSRGHIFDKSTCN 266
           IS+GPCQTPTLGFCVERHDKI++FKPE YW+L   ++ +   ++ + W R  +FD     
Sbjct: 212 ISFGPCQTPTLGFCVERHDKIQSFKPETYWVLQAKVHTDKEESLLLDWDRVRVFDWEIAQ 271

Query: 267 VFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQ 326
           +F    + EK   V       K+K +P ALNTVE++RVASS LGMGP HAMQIAERLYTQ
Sbjct: 272 MFLNMTKLEKEAWVEATSRKEKAKQRPLALNTVEMLRVASSALGMGPQHAMQIAERLYTQ 331

Query: 327 GYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVGDHPPIT 386
           GY+SYPRTETT YPENFDL   LRQQ + P W D V+++L+ GI++PRKG D GDHPPIT
Sbjct: 332 GYISYPRTETTHYPENFDLKGSLRQQANHPYWADSVKQLLAEGINRPRKGHDAGDHPPIT 391

Query: 387 PTKLATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPG 446
           P K AT  +L GDAWRLY+YI RHFI T+  D  Y Q    F +  E FT   K ++ PG
Sbjct: 392 PMKSATEAELGGDAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPEHFTCMGKTVISPG 451

Query: 447 FTGVMTWSAMK-NESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTD 505
           FT +M W ++   ES+P  + GD   +  VKM+E++T+PPDYLTE+ELI+LMEKHGIGTD
Sbjct: 452 FTEIMPWQSVPLEESLPTCQKGDTFTVGEVKMLEKQTSPPDYLTEAELITLMEKHGIGTD 511

Query: 506 ASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRVQ 561
           ASIPVHINNICQRNYVTV SGRRL PT+LGIVLVHGY KID ELV PT+RSA   Q
Sbjct: 512 ASIPVHINNICQRNYVTVESGRRLKPTNLGIVLVHGYYKIDAELVLPTIRSAVEKQ 567

Releases the supercoiling and torsional tension of DNA introduced during the DNA replication and transcription by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand than undergoes passage around the unbroken strand thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone (By similarity). Possesses negatively supercoiled DNA relaxing activity.

Mus musculus (taxid: 10090)

EC: 5

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: .

EC: 2

>sp|O96651|TOP3B_DROME DNA topoisomerase 3-beta OS=Drosophila melanogaster GN=Top3beta PE=2 SV=2

 Score =  681 bits (1757), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 332/527 (62%), Positives = 394/527 (74%), Gaps = 8/527 (1%)

Query: 34  ACSVHEWVGPLFGD-LVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPTEKREATP 92
            CS HEW G    +  V F+MTSVCGH+M LDF  KYN WDKVDP++LF C TEK+E  P
Sbjct: 35  GCSTHEWTGNFRNEGSVHFRMTSVCGHVMSLDFNKKYNCWDKVDPIQLFGCATEKKETNP 94

Query: 93  KLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQIN-INSPKTVWRARFSAI 151
           K  +  FLA+EA+ C++LVLWLDCDKEGENICFEVM+AV+H IN + S +  +RA FSAI
Sbjct: 95  KQNMRKFLAHEARGCDYLVLWLDCDKEGENICFEVMDAVKHVINNVYSDQVTYRAHFSAI 154

Query: 152 TDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYG 211
           T+KDIK AM  L  PN  EA+SVDARQELDLRIGCAFTR+QTKFFQ +YGDLD+SLISYG
Sbjct: 155 TEKDIKKAMETLGHPNENEAKSVDARQELDLRIGCAFTRFQTKFFQDRYGDLDSSLISYG 214

Query: 212 PCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNGV-AVSVTWSRGHIFDKSTCNVFFK 270
           PCQTPTLGFCV+RHD I+TFKPE +W L L   L G   V++ W+RG +F K    +   
Sbjct: 215 PCQTPTLGFCVKRHDDIQTFKPESFWHLQL---LAGQPEVTLEWARGRVFKKDIAIMLLN 271

Query: 271 AVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVS 330
            V++ K  TV  V S    K+KPQALNTVELMR+ SSGLG+GP  AMQIAERLYTQGY+S
Sbjct: 272 RVKEHKKATVESVASKEAYKSKPQALNTVELMRICSSGLGIGPFQAMQIAERLYTQGYIS 331

Query: 331 YPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVGDHPPITPTKL 390
           YPRTET QYP NFDL AVL   + S D+G+  R +L + I  PRKGKD GDHPPITP KL
Sbjct: 332 YPRTETNQYPTNFDLPAVLHVLKPSADFGEEARSILGD-IQTPRKGKDAGDHPPITPMKL 390

Query: 391 ATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGV 450
             R+  D D WR+Y++I RHF+GT+  DL Y    AK SV  E F+  A  L+  GFT V
Sbjct: 391 GNRSDFDRDTWRVYEFICRHFMGTVSRDLKYRVTTAKLSVGMETFSCTASVLIDAGFTKV 450

Query: 451 MTWSAM-KNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIP 509
           MTWSA  K+E  P F  G  + I  V+++E +T PPDYLTESELI+LME+HGIGTDASIP
Sbjct: 451 MTWSAFGKDEPQPPFVQGTQVAINDVRLIESQTGPPDYLTESELITLMEEHGIGTDASIP 510

Query: 510 VHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRS 556
           VHINNICQRNYV + +GR+L+PT+LGIVLVHGYQKID ELV PTMR+
Sbjct: 511 VHINNICQRNYVHIENGRKLMPTTLGIVLVHGYQKIDPELVLPTMRT 557

Releases the supercoiling and torsional tension of DNA introduced during the DNA replication and transcription by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand than undergoes passage around the unbroken strand thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone (By similarity). Weakly relaxes negative supercoils and displays a distinct preference for binding single-stranded DNA.

Drosophila melanogaster (taxid: 7227)

EC: 5

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: .

EC: 2

>sp|O70157|TOP3A_MOUSE DNA topoisomerase 3-alpha OS=Mus musculus GN=Top3a PE=1 SV=1

 Score =  385 bits (990), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 218/559 (38%), Positives = 316/559 (56%), Gaps = 12/559 (2%)

Query: 5   VKKLVPASEIKLARPSLISLLTP--LQRMNGACS---VHEWVGPLFGDLVLFKMTSVCGH 59
           V+K++  +E   A   +  LL+   ++R  G      ++E+   L+G  V   MTSV GH
Sbjct: 33  VRKVLCVAEKNDAAKGIADLLSNGRMRRKEGLSKFNKIYEFDYHLYGQNVTMIMTSVSGH 92

Query: 60  IMGLDFTSKYNNWDKVDPLELFSCPTEKREATPKLKLPAFLANEAKDCEFLVLWLDCDKE 119
           ++  DF  ++  W   +PL LF    EK      + +   L  E   C+ LV+W DCD+E
Sbjct: 93  LLAHDFQMQFRKWQSCNPLVLFEAEIEKYCPENFIDIKKTLERETHHCQALVIWTDCDRE 152

Query: 120 GENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNLVKPNIFEARSVDARQE 179
           GENI FE++   +    +     V RARFS IT   ++ A  NL +P+   + +VD RQE
Sbjct: 153 GENIGFEIIHVCK---AVKPNLRVLRARFSEITPHAVRTACENLTEPDQRVSDAVDVRQE 209

Query: 180 LDLRIGCAFTRYQTKFFQGKYGD-LDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWL 238
           LDLRIG AFTR+QT   Q  + + L   LISYG CQ PTLGF VER   I+ F PE +  
Sbjct: 210 LDLRIGAAFTRFQTLRLQRIFPEVLAEQLISYGSCQFPTLGFVVERFKAIQAFVPEVFHK 269

Query: 239 LDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNT 298
           + +T +     V   W R  +F+ + C V ++   ++   TVV+V+S  KSK +PQAL+T
Sbjct: 270 IKVTHDHKDGTVEFNWKRYRLFNHTACLVLYQLCMEDPMATVVEVRSKPKSKWRPQALDT 329

Query: 299 VELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENFDLVAVLRQQESSPDW 358
           VEL ++AS  L +     M+IAE+LYTQGY+SYPRTET  +P++ +LVA++ QQ   P W
Sbjct: 330 VELEKLASRKLRINAKETMRIAEKLYTQGYISYPRTETNIFPKDLNLVALVEQQTVDPHW 389

Query: 359 GDHVREVLSNGISKPRKG-KDVGDHPPITPTKLATRTQLDGDAWRLYDYIVRHFIGTLCG 417
           G   + +L  G   PR G K    HPPI PTK    + L GD  RLY++IVRHF+     
Sbjct: 390 GAFAQTILERGGPTPRNGSKSDQAHPPIHPTKYT--SGLQGDDRRLYEFIVRHFLACCSQ 447

Query: 418 DLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKM 477
           D    +   +  +A E F      +L   +  V  +    ++ +P ++ G      +V+M
Sbjct: 448 DAQGQETTVEIDIAQERFVAHGLIILARNYLDVYPYDHWSDKLLPVYEQGSHFQPSTVEM 507

Query: 478 VERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIV 537
           V+ +T+PP  LTE++LI+LMEKHGIGTDA+   HI  I  R YV +TS +R +P  LG+ 
Sbjct: 508 VDGETSPPQLLTEADLIALMEKHGIGTDATHAEHIETIKARMYVGLTSDKRFLPGHLGMG 567

Query: 538 LVHGYQKIDRELVEPTMRS 556
           LV GY  +  E+ +P +R+
Sbjct: 568 LVEGYDSMGYEMSKPDLRA 586

Releases the supercoiling and torsional tension of DNA introduced during the DNA replication and transcription by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand than undergoes passage around the unbroken strand thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone. Essential component of the RMI complex, a complex that plays an important role in the processing of homologous recombination intermediates to limit DNA crossover formation in cells.

Mus musculus (taxid: 10090)

EC: 5

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: .

EC: 2

>sp|Q13472|TOP3A_HUMAN DNA topoisomerase 3-alpha OS=Homo sapiens GN=TOP3A PE=1 SV=1

 Score =  382 bits (981), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 218/564 (38%), Positives = 315/564 (55%), Gaps = 13/564 (2%)

Query: 1   MHLR-VKKLVPASEIKLARPSLISLLTP--LQRMNGACS---VHEWVGPLFGDLVLFKMT 54
           M LR V+K++  +E   A   +  LL+   ++R  G      ++E+   L+G  V   MT
Sbjct: 28  MALRGVRKVLCVAEKNDAAKGIADLLSNGRMRRREGLSKFNKIYEFDYHLYGQNVTMVMT 87

Query: 55  SVCGHIMGLDFTSKYNNWDKVDPLELFSCPTEKREATPKLKLPAFLANEAKDCEFLVLWL 114
           SV GH++  DF  ++  W   +PL LF    EK      + +   L  E + C+ LV+W 
Sbjct: 88  SVSGHLLAHDFQMQFRKWQSCNPLVLFEAEIEKYCPENFVDIKKTLERETRQCQALVIWT 147

Query: 115 DCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNLVKPNIFEARSV 174
           DCD+EGENI FE++   +    +     V RARFS IT   ++ A  NL +P+   + +V
Sbjct: 148 DCDREGENIGFEIIHVCK---AVKPNLQVLRARFSEITPHAVRTACENLTEPDQRVSDAV 204

Query: 175 DARQELDLRIGCAFTRYQTKFFQGKYGD-LDASLISYGPCQTPTLGFCVERHDKIRTFKP 233
           D RQELDLRIG AFTR+QT   Q  + + L   LISYG CQ PTLGF VER   I+ F P
Sbjct: 205 DVRQELDLRIGAAFTRFQTLRLQRIFPEVLAEQLISYGSCQFPTLGFVVERFKAIQAFVP 264

Query: 234 EPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKP 293
           E +  + +T +     V   W R  +F+ + C V ++   ++   TVV+V+S  KSK +P
Sbjct: 265 EIFHRIKVTHDHKDGIVEFNWKRHRLFNHTACLVLYQLCVEDPMATVVEVRSKPKSKWRP 324

Query: 294 QALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENFDLVAVLRQQE 353
           QAL+TVEL ++AS  L +     M+IAE+LYTQGY+SYPRTET  +P + +L  ++ QQ 
Sbjct: 325 QALDTVELEKLASRKLRINAKETMRIAEKLYTQGYISYPRTETNIFPRDLNLTVLVEQQT 384

Query: 354 SSPDWGDHVREVLSNGISKPRKG-KDVGDHPPITPTKLATRTQLDGDAWRLYDYIVRHFI 412
             P WG   + +L  G   PR G K    HPPI PTK      L GD  RLY++IVRHF+
Sbjct: 385 PDPRWGAFAQSILERGGPTPRNGNKSDQAHPPIHPTKYT--NNLQGDEQRLYEFIVRHFL 442

Query: 413 GTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNESIPDFKPGDLIPI 472
                D    +   +  +A E F      +L   +  V  +    ++ +P ++ G     
Sbjct: 443 ACCSQDAQGQETTVEIDIAQERFVAHGLMILARNYLDVYPYDHWSDKILPVYEQGSHFQP 502

Query: 473 QSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPT 532
            +V+MV+ +T+PP  LTE++LI+LMEKHGIGTDA+   HI  I  R YV +T  +R +P 
Sbjct: 503 STVEMVDGETSPPKLLTEADLIALMEKHGIGTDATHAEHIETIKARMYVGLTPDKRFLPG 562

Query: 533 SLGIVLVHGYQKIDRELVEPTMRS 556
            LG+ LV GY  +  E+ +P +R+
Sbjct: 563 HLGMGLVEGYDSMGYEMSKPDLRA 586

Releases the supercoiling and torsional tension of DNA introduced during the DNA replication and transcription by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand than undergoes passage around the unbroken strand thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone (By similarity). Essential component of the RMI complex, a complex that plays an important role in the processing of homologous recombination intermediates to limit DNA crossover formation in cells.

Homo sapiens (taxid: 9606)

EC: 5

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: .

EC: 2

>sp|O61660|TOP3_CAEEL DNA topoisomerase 3 OS=Caenorhabditis elegans GN=top-3 PE=2 SV=1

 Score =  366 bits (940), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 196/524 (37%), Positives = 289/524 (55%), Gaps = 12/524 (2%)

Query: 44  LFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPTEKREATPKLKL-PAFLAN 102
           LFG      +TSV GH+M   F    +NW     +ELF  P  +   TP++KL    L  
Sbjct: 45  LFGQQTAISVTSVSGHMMNFQFHENMSNWQTASMVELFRAPV-RHVVTPEMKLIEQTLRE 103

Query: 103 EAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWN 162
           +A+  + LV+W DCD+EGE I  E+++  R   + N    ++RARFS IT   I  A  N
Sbjct: 104 QAQRHDILVVWTDCDREGEAIGAEIVKVCR---DSNRRLDIFRARFSEITKAAITRAARN 160

Query: 163 LVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDL-----DASLISYGPCQTPT 217
           L++ +     +VD R ELDLRIG AFTR QT   + ++ DL      + +ISYG CQ PT
Sbjct: 161 LIRLDEKTVAAVDCRSELDLRIGSAFTRLQTLHLRNRFRDLLGQNDTSQVISYGSCQFPT 220

Query: 218 LGFCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKH 277
           LGF  +R+  I  F  EP+W L +        V   W R  +FD+ T ++     ++ K 
Sbjct: 221 LGFVTDRYKMIENFVSEPFWKLIVEHTRESHKVEFLWDRNRLFDRDTVDILHDECKETKE 280

Query: 278 VTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETT 337
             V  V    KSK +PQAL+TVEL ++  S L M     MQ+AE+LY++G++SYPRTET 
Sbjct: 281 AHVEKVAKKPKSKWRPQALDTVELEKLGISKLRMSAKQTMQVAEKLYSKGFISYPRTETN 340

Query: 338 QYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVGD-HPPITPTKLATRTQL 396
           ++P   +L  +++QQ  S  WGD   EVL NG++ PR G+   + HPPI P K   + QL
Sbjct: 341 KFPAGLNLTPLVQQQTQSNIWGDFANEVLQNGVN-PRNGRKSDEAHPPIHPLKFTEKHQL 399

Query: 397 DGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAM 456
            GD W++Y+ +VRHF+  +  D    + +   +V  E F      +   G+  V  +   
Sbjct: 400 QGDDWKVYELVVRHFLACVSQDAQGEETMVNLTVGTEKFHASGLRIRDMGYLKVYVYEKW 459

Query: 457 KNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNIC 516
            N  +P +  G+      +K+ + KT  PD+LTE++LISLM+K+GIGTDA+   HI  I 
Sbjct: 460 GNRLLPTYTEGERFTDFELKIGDGKTQAPDFLTEADLISLMDKYGIGTDATHAEHIEKIK 519

Query: 517 QRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRV 560
            R Y+ V    +L+P+ LG+ LV GY  +   + +P +R+   +
Sbjct: 520 TREYIGVRPDGKLIPSFLGLALVDGYDDMGFAMSKPDLRANLEI 563

Releases the supercoiling and torsional tension of DNA introduced during the DNA replication and transcription by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand than undergoes passage around the unbroken strand thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone.

Caenorhabditis elegans (taxid: 6239)

EC: 5

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: .

EC: 2

>sp|Q9NG98|TOP3A_DROME DNA topoisomerase 3-alpha OS=Drosophila melanogaster GN=Top3alpha PE=2 SV=2

 Score =  348 bits (892), Expect = 8e-95,   Method: Compositional matrix adjust.
 Identities = 195/531 (36%), Positives = 283/531 (53%), Gaps = 16/531 (3%)

Query: 37  VHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPTEKREATPKLKL 96
           V ++  P+ G      MTSV GH+M L F   Y NW  VDP  LF  P +K   +    +
Sbjct: 62  VFDFEAPVRGQNAKMVMTSVSGHMMQLAFQVSYKNWRTVDPRSLFDAPVKKGVGSDYEPI 121

Query: 97  PAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDI 156
              L  E + C+ L++W DCD+EGENI +E+++  R    I    +V+RA FS IT   +
Sbjct: 122 KRTLEREVRGCQGLIIWTDCDREGENIGYEIIDVCRA---IKPNISVYRATFSEITTVAV 178

Query: 157 KAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQT----KFFQGKYGDLDASLISYGP 212
           + A+  L +P+  ++ +VD R ELDLR G A TR+QT    + F  K  D    LISYG 
Sbjct: 179 RRALQQLGQPDKRQSDAVDVRTELDLRTGAAITRFQTMRLQRLFPEKIAD---KLISYGS 235

Query: 213 CQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTCN--VFFK 270
           CQ PTLGF  ER+ +I  F  EP+W + +   ++ + V   W+R  +FDK  C   +   
Sbjct: 236 CQIPTLGFVAERYKEIEAFVSEPFWKIKVLHTIDDLTVEFNWARNRLFDKEACENYLLLC 295

Query: 271 AVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVS 330
             E +    V  V    K K +P  L+TVE+ ++ S  L +     M IAE+LYT+G++S
Sbjct: 296 LAEPDPRALVESVTVKPKHKWRPTPLDTVEMEKLGSRKLKLSAKETMTIAEKLYTKGFIS 355

Query: 331 YPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKG-KDVGDHPPITPTK 389
           YPRTET Q+ + F L  ++  Q    DWG   + V+  G   PR G K    HPPI PTK
Sbjct: 356 YPRTETNQFSKEFALAPLVEMQTGHRDWGAFAQRVIEWG-PNPRNGNKSDQAHPPIHPTK 414

Query: 390 LATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTG 449
           LA    L G+  R+Y+ +VRHF+  +  D V ++ +    +A E FT     +    +  
Sbjct: 415 LAE--NLQGNEARVYELVVRHFLACVSKDAVGSETLVHIDIAGEKFTANGLVIHERNYLD 472

Query: 450 VMTWSAMKNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIP 509
           V  +     + I  ++ G       V + E  TT P  LTE++LI+LMEKHGIGTDA+  
Sbjct: 473 VYVYDKWSAKQIHHYENGQRFEPTEVSLHEGATTAPPLLTEADLIALMEKHGIGTDATHA 532

Query: 510 VHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRV 560
            HIN I +R Y+ V     LVP  +G+ L  GY  ++  L +P +R+ + +
Sbjct: 533 EHINTIKERGYIGVLDKGFLVPGVIGMGLYEGYDAMELALAKPQLRAEFEL 583

Releases the supercoiling and torsional tension of DNA introduced during the DNA replication and transcription by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand than undergoes passage around the unbroken strand thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone (By similarity). Weakly relaxes negative supercoils and displays a distinct preference for binding single-stranded DNA.

Drosophila melanogaster (taxid: 7227)

EC: 5

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: .

EC: 2

>sp|Q8T2T7|TOP3_DICDI DNA topoisomerase 3 OS=Dictyostelium discoideum GN=top3 PE=3 SV=1

 Score =  338 bits (866), Expect = 1e-91,   Method: Compositional matrix adjust.
 Identities = 189/539 (35%), Positives = 286/539 (53%), Gaps = 41/539 (7%)

Query: 53  MTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPTEKREATPKLKLPAFLANEAKDCEFLVL 112
            TSV GH+M +D   ++  W   DP++LF  P  K   + K  L   L  E K  + L+L
Sbjct: 56  FTSVTGHLMEIDVVEQFKPWASCDPIQLFDAPIRKTVPSDKEPLKKTLEREIKKADILIL 115

Query: 113 WLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNLVKPNIFEAR 172
           WLDCD+EGENI FEV+E  +   N       +RA FSAI  ++I  A  NL KPN  ++ 
Sbjct: 116 WLDCDREGENIAFEVLEVCK---NAKKKFEFYRAHFSAIIPREIDRACKNLAKPNEKDSI 172

Query: 173 SVDARQELDLRIGCAFTRYQTKFFQGKYGDLDAS-------------------------- 206
           +VD R E+DLRIG AFTR+QT + + K+  +  S                          
Sbjct: 173 AVDTRMEIDLRIGAAFTRFQTLYLK-KFKIISNSDNQPKTTTPANGNILNNSNNNSSGKE 231

Query: 207 LISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDL------TLNLNGVAVSVTWSRGHIF 260
           +ISYGPCQ PTLGF VER+ +I  FKPE +W L +      T +   + V+ +W R  +F
Sbjct: 232 IISYGPCQFPTLGFVVERYFRIVNFKPEDFWHLSVVHEKMDTSSGKMIPVTFSWCRNRLF 291

Query: 261 DKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIA 320
           D +   + ++        TVVDV +S +S+ +P  L T+EL + AS  L +     MQ A
Sbjct: 292 DYTAAFILYEKCLDNTEATVVDV-TSKESRYRPVPLTTIELQKAASKKLRISSVQTMQYA 350

Query: 321 ERLYTQGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNG-ISKPRKGKDV 379
           E LYT+G +SYPRTET  +    DL  ++  Q S+P+WG +   +++N     P+ GK+ 
Sbjct: 351 EELYTKGLISYPRTETDSFQAGTDLKGLIGNQASNPEWGAYASRLINNNQFVYPKSGKNN 410

Query: 380 GD-HPPITPTKLATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTME 438
            + HPPI PT  AT   L G+  ++YD+I R F+     + V+        +  E F+  
Sbjct: 411 DNSHPPIHPTSSAT--GLSGNLKKIYDFITRRFLACCSEESVFANTTVTIDIQGERFSET 468

Query: 439 AKYLLHPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLME 498
              +L  G+  V  +    ++ IP ++ G+    + + + +  T  P Y+TE+EL++ M+
Sbjct: 469 GTMVLKLGYLEVYPFDKRNDKLIPTYQKGERFTPKRIDLTKGTTVAPHYITEAELLTAMD 528

Query: 499 KHGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSA 557
            + IGTDA++  HI  I  R YV      + VP++LG+ LV  Y+ +  E  +P +R+A
Sbjct: 529 NNKIGTDATMATHIQTIQDRFYVKKNESNQFVPSNLGVSLVASYELMGFEFSKPNLRAA 587

Releases the supercoiling and torsional tension of DNA introduced during the DNA replication and transcription by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand than undergoes passage around the unbroken strand thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone.

Dictyostelium discoideum (taxid: 44689)

EC: 5

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: .

EC: 2

>sp|O60126|TOP3_SCHPO DNA topoisomerase 3 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=top3 PE=1 SV=2

 Score =  296 bits (758), Expect = 3e-79,   Method: Compositional matrix adjust.
 Identities = 169/519 (32%), Positives = 268/519 (51%), Gaps = 13/519 (2%)

Query: 53  MTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPTEKREATPKLKLPAFLANEAKDCEFLVL 112
           MTSV GH+    F S+Y++W  V    LF        +     L   +  EA++ ++L +
Sbjct: 55  MTSVSGHLTEASFPSEYSSWSSVPQDVLFDAQIITSVSKNAEVLADNIKKEARNAQYLYI 114

Query: 113 WLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNLVKPNIFEAR 172
           W DCD+EGE+I  E+    R     N    V RA F+ +    I +A       +   A 
Sbjct: 115 WTDCDREGEHIGVEISNVARAS---NPSIQVIRADFNNLERSHIISAAKRPRDVSKNAAD 171

Query: 173 SVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFK 232
           +VDAR ELD R+G  FTR QT   Q  +  L   +ISYGPCQ PTLGF V+R  ++  F 
Sbjct: 172 AVDARIELDFRLGAIFTRLQTIQLQKSFDILQNKIISYGPCQFPTLGFVVDRWQRVEDFV 231

Query: 233 PEPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTK 292
           PE YW L       G  +   W R  +FD+ T  +  +   + K   VV++    K+K K
Sbjct: 232 PETYWHLRFVDKRQGKTIQFNWERAKVFDRLTTMIILENCLECKTAKVVNITQKPKTKYK 291

Query: 293 PQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENFDLVAVLRQQ 352
           P  L+TVEL ++    L +     +++AE LYT G+VSYPRTET Q+  + +L A++++ 
Sbjct: 292 PLPLSTVELTKLGPKHLRISAKKTLELAENLYTNGFVSYPRTETDQFDSSMNLHAIIQKL 351

Query: 353 ESSPDWGDHVREVLSNGISKPRKGK-DVGDHPPITPTKLATRTQL-DGDAWRLYDYIVRH 410
             + +W  +   +L+     PRKGK +   HPPI P ++  R+ L   D W++Y+ I R 
Sbjct: 352 TGAQEWDSYAEGLLAGDYRPPRKGKHNDRAHPPIHPVQMVHRSALPSQDHWKVYELITRR 411

Query: 411 FIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMK-NESIPDFKPGDL 469
           F+     +    + + +  + +E+F+ +   +    +  V  +   + ++ +P+++  + 
Sbjct: 412 FLACCSDNAKGAETLVQVKMEEELFSKKGLLVTEKNYLEVYPYEKWESSDQLPEYRLHEE 471

Query: 470 IPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGR-- 527
                + M++  T+ P Y+TE ELI+LM+ +GIGTDA++  HI  + +R YV     R  
Sbjct: 472 FQPHILDMMDSSTSSPSYITEPELIALMDANGIGTDATMAEHIEKVQEREYVIKRKKRGQ 531

Query: 528 ---RLVPTSLGIVLVHGYQKIDRE--LVEPTMRSAYRVQ 561
                VP+SLG+ L  GY +I  E  L +P +R    VQ
Sbjct: 532 GVTEFVPSSLGVALAKGYDEIGLEWSLTKPFLRKEMEVQ 570

Releases the supercoiling and torsional tension of DNA introduced during the DNA replication and transcription by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand than undergoes passage around the unbroken strand thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

EC: 5

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: .

EC: 2

>sp|P13099|TOP3_YEAST DNA topoisomerase 3 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=TOP3 PE=1 SV=1

 Score =  284 bits (727), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 175/537 (32%), Positives = 268/537 (49%), Gaps = 41/537 (7%)

Query: 53  MTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPTEKREATPKLKLPAFLANEAKDCEFLVL 112
           MTSV GH+ G+DF+   + W K    ELF  P  +     + K+ + +  EA++ ++L++
Sbjct: 58  MTSVAGHLTGIDFSHDSHGWGKCAIQELFDAPLNEIMNNNQKKIASNIKREARNADYLMI 117

Query: 113 WLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNLVKPNIFEAR 172
           W DCD+EGE I +E+ +  +    +     V+RA FS +  + I  A  N  + ++    
Sbjct: 118 WTDCDREGEYIGWEIWQEAKRGNRLIQNDQVYRAVFSHLERQHILNAARNPSRLDMKSVH 177

Query: 173 SVDARQELDLRIGCAFTRYQTKFFQGKYGDL----------------DASLISYGPCQTP 216
           +V  R E+DLR G  FTR  T+  + K  +                 D+ ++SYG CQ P
Sbjct: 178 AVGTRIEIDLRAGVTFTRLLTETLRNKLRNQATMTKDGAKHRGGNKNDSQVVSYGTCQFP 237

Query: 217 TLGFCVERHDKIRTFKPEPYWLLDLTLNL--NGVAVSVTWSRGHIFDKSTCNVFFKA-VE 273
           TLGF V+R ++IR F PE +W + L +    NG   +  W RGH+FD+ +   F++  +E
Sbjct: 238 TLGFVVDRFERIRNFVPEEFWYIQLVVENKDNGGTTTFQWDRGHLFDRLSVLTFYETCIE 297

Query: 274 KEKHVT-VVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYP 332
              +V  VVD++S   +K +P  L TVEL +  +  L +    ++  AE+LY +G++SYP
Sbjct: 298 TAGNVAQVVDLKSKPTTKYRPLPLTTVELQKNCARYLRLNAKQSLDAAEKLYQKGFISYP 357

Query: 333 RTETTQYPENFDLVAVLRQQE--------SSPDWGDHVREVL-------SNGISKPRKGK 377
           RTET  +P   DL +++ +Q             W  +   +L       +N    PR G 
Sbjct: 358 RTETDTFPHAMDLKSLVEKQAQLDQLAAGGRTAWASYAASLLQPENTSNNNKFKFPRSGS 417

Query: 378 -DVGDHPPITP-TKLATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMF 435
            D   HPPI P   L     +     R+Y+Y+ RHF+     D            A E F
Sbjct: 418 HDDKAHPPIHPIVSLGPEANVSPVERRVYEYVARHFLACCSEDAKGQSMTLVLDWAVERF 477

Query: 436 TMEAKYLLHPGFTGVMTWSAMK-NESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELI 494
           +     +L   F  V  W+  +  + +P  +   L+ I   +M    T PP  +TESELI
Sbjct: 478 SASGLVVLERNFLDVYPWARWETTKQLPRLEMNALVDIAKAEMKAGTTAPPKPMTESELI 537

Query: 495 SLMEKHGIGTDASIPVHINNICQRNYV---TVTSGRRLVPTSLGIVLVHGYQKIDRE 548
            LM+ +GIGTDA+I  HI+ I  RNYV    V     L PT+LG+ LVHG++ I  E
Sbjct: 538 LLMDTNGIGTDATIAEHIDKIQVRNYVRSEKVGKETYLQPTTLGVSLVHGFEAIGLE 594

Releases the supercoiling and torsional tension of DNA introduced during the DNA replication and transcription by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand than undergoes passage around the unbroken strand thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone (By similarity). Essential for proper chromosome segregation in both meiosis and mitosis. Weakly relaxes negative supercoils and displays a distinct preference for binding single-stranded DNA. The TOP3-SGS1 protein complex may function as a eukaryotic reverse gyrase introducing positive supercoils into extrachromosomal ribosomal DNA rings.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

EC: 5

EC: .

EC: 9

EC: 9

EC: .

EC: 1

EC: .

EC: 2

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	562
156551898	852	PREDICTED: DNA topoisomerase 3-beta-1-li	0.943	0.622	0.694	0.0
91081101	852	PREDICTED: similar to prokaryotic DNA to	0.943	0.622	0.676	0.0
66509929	851	PREDICTED: DNA topoisomerase 3-beta-1-li	0.953	0.629	0.671	0.0
380025214	851	PREDICTED: DNA topoisomerase 3-beta-1 [A	0.953	0.629	0.669	0.0
383857261	851	PREDICTED: DNA topoisomerase 3-beta-1-li	0.953	0.629	0.669	0.0
307184245	851	DNA topoisomerase 3-beta-1 [Camponotus f	0.939	0.620	0.672	0.0
340722711	851	PREDICTED: DNA topoisomerase 3-beta-1-li	0.953	0.629	0.664	0.0
350424370	851	PREDICTED: DNA topoisomerase 3-beta-1-li	0.953	0.629	0.664	0.0
307203099	851	DNA topoisomerase 3-beta-1 [Harpegnathos	0.944	0.623	0.666	0.0
332027377	848	DNA topoisomerase 3-beta-1 [Acromyrmex e	0.934	0.619	0.661	0.0

>gi|156551898|ref|XP_001606777.1| PREDICTED: DNA topoisomerase 3-beta-1-like [Nasonia vitripennis]

 Score =  790 bits (2041), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 370/533 (69%), Positives = 431/533 (80%), Gaps = 3/533 (0%)

Query: 32  NGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPTEKREAT 91
           NG+CSVHEW+G    + V FKMTSVCGH+M LDF  KYNNWDKVDP ELFSCPTEK+EA 
Sbjct: 33  NGSCSVHEWLGQFRSETVNFKMTSVCGHVMSLDFIGKYNNWDKVDPAELFSCPTEKKEAV 92

Query: 92  PKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININ-SPKTVWRARFSA 150
           PKLK+P+FLA E   C++LVLWLDCDKEGENICFEV++AV+       +P  +WRA+FSA
Sbjct: 93  PKLKIPSFLAKEGGYCDYLVLWLDCDKEGENICFEVIQAVQQGSTRRLNPNDIWRAKFSA 152

Query: 151 ITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISY 210
           ITDKDIKAA+ NL KPN  EARSVDARQELDLRIGCAFTR+QTKFFQGKYGDLDASLISY
Sbjct: 153 ITDKDIKAALANLAKPNENEARSVDARQELDLRIGCAFTRFQTKFFQGKYGDLDASLISY 212

Query: 211 GPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTL-NLNGVAVSVTWSRGHIFDKSTCNVFF 269
           GPCQTPTLGFCV+RHD+I+TFKP+PYW+L +T+   +G+ V ++WSR   FDK   N+F 
Sbjct: 213 GPCQTPTLGFCVQRHDEIQTFKPDPYWVLQVTVKTADGLDVVLSWSRVRSFDKEVANIFL 272

Query: 270 KAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYV 329
             V++  H TV  +QS+ KSK +P ALNTVELMRVASSGLGMGPHHAMQIAERLYTQGY+
Sbjct: 273 SHVKEHDHATVTSIQSTEKSKARPIALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYI 332

Query: 330 SYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVGDHPPITPTK 389
           SYPRTETT YPENFDLV+ L+QQ++S DWGD VR +LS+GISKP+KG D GDHPPITP K
Sbjct: 333 SYPRTETTSYPENFDLVSTLKQQQNSSDWGDEVRRILSSGISKPKKGHDAGDHPPITPMK 392

Query: 390 LATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTG 449
            A+R +LDGD+WRLYDYI RHFI TL  D  Y    AKF +  E F++    L+ PG+T 
Sbjct: 393 SASRNELDGDSWRLYDYITRHFIATLAKDCKYLSTTAKFEIGMETFSVTGHSLIDPGYTS 452

Query: 450 VMTWSAM-KNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASI 508
           ++TW A+  NES+P F  G+ + IQ  K++E  T PPDYLTESELI+LMEKHGIGTDASI
Sbjct: 453 LLTWQALSNNESLPRFSIGERVKIQESKLLECFTQPPDYLTESELITLMEKHGIGTDASI 512

Query: 509 PVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRVQ 561
           PVHINNIC RNYV V +GR+LVPTSLGIVLVHGYQKID ELV PTMRSA   Q
Sbjct: 513 PVHINNICIRNYVNVATGRKLVPTSLGIVLVHGYQKIDPELVLPTMRSAVEEQ 565

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|91081101|ref|XP_975504.1| PREDICTED: similar to prokaryotic DNA topoisomerase [Tribolium castaneum] gi|270005298|gb|EFA01746.1| hypothetical protein TcasGA2_TC007344 [Tribolium castaneum]

 Score =  778 bits (2010), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 361/534 (67%), Positives = 432/534 (80%), Gaps = 4/534 (0%)

Query: 32  NGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPTEKREAT 91
           NG CSVHEW G   G     KMTSVCGH+MG+DF SKYNNWD+VDP+ELFSCP EK+EAT
Sbjct: 33  NGICSVHEWNGTFQGAPARLKMTSVCGHVMGVDFISKYNNWDRVDPVELFSCPIEKKEAT 92

Query: 92  PKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQIN--INSPKTVWRARFS 149
           PK K+PAFL++EAK C++LVLWLDCDKEGENICFEVM +V   +N  + S K  +RARFS
Sbjct: 93  PKFKMPAFLSHEAKGCDYLVLWLDCDKEGENICFEVMNSVARSMNGDVYSDKVTFRARFS 152

Query: 150 AITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLIS 209
           AITDKDIKAA  NL  PN  EARSVDARQELDLRIGCAFTR+QTKFFQG+YGDLD+SLIS
Sbjct: 153 AITDKDIKAAFNNLAHPNENEARSVDARQELDLRIGCAFTRFQTKFFQGRYGDLDSSLIS 212

Query: 210 YGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTL-NLNGVAVSVTWSRGHIFDKSTCNVF 268
           YGPCQTPTLGFCV+RHD+I+TFKPE YW++  T+   +G  V + W R   FDK   N+F
Sbjct: 213 YGPCQTPTLGFCVQRHDQIQTFKPEAYWVIKATIVTKDGNDVHLDWKRVRCFDKEVANMF 272

Query: 269 FKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGY 328
            + ++ +KH  V++V S  K+K++P ALNTVELMRVASSGLGMGPHHAMQIAE+LYTQGY
Sbjct: 273 LQQIKDQKHAKVLNVSSKEKAKSRPVALNTVELMRVASSGLGMGPHHAMQIAEKLYTQGY 332

Query: 329 VSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVGDHPPITPT 388
           +SYPRTETT+YPENFDLV VLRQQ++S +WGD VRE+LS G+++P++G D GDHPPITP 
Sbjct: 333 ISYPRTETTRYPENFDLVGVLRQQQNSTEWGDEVREILSRGVNRPKQGHDAGDHPPITPM 392

Query: 389 KLATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFT 448
           K ATR + D D+W+LYDYI RHFIGTL  D  Y    A  ++ +E+FT+  K LL PGFT
Sbjct: 393 KSATRNEFDSDSWKLYDYITRHFIGTLARDCKYLSTTATIAINEEIFTVTGKTLLDPGFT 452

Query: 449 GVMTWSAM-KNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDAS 507
            VMTW A+ KNE +P+    + +PI+ +++ E +T+PPDYLTE+ELI+LME HGIGTDAS
Sbjct: 453 SVMTWQALDKNEIVPNLTENESVPIKDMRLTEHQTSPPDYLTEAELITLMETHGIGTDAS 512

Query: 508 IPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRVQ 561
           IPVHINNICQRNYVTVT+GR+L PT+LGIVLVHGYQKID ELV PTMRSA   Q
Sbjct: 513 IPVHINNICQRNYVTVTAGRKLKPTTLGIVLVHGYQKIDAELVLPTMRSAVEEQ 566

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|66509929|ref|XP_625165.1| PREDICTED: DNA topoisomerase 3-beta-1-like isoform 2 [Apis mellifera]

 Score =  778 bits (2010), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 362/539 (67%), Positives = 435/539 (80%), Gaps = 3/539 (0%)

Query: 26  TPLQRMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPT 85
           T  + +NG+CSVHEW+G    + V FKMTSV GH+M LDF  KYNNWDKVDP ELFSCPT
Sbjct: 27  TSRKGLNGSCSVHEWIGQFRSETVNFKMTSVFGHVMTLDFIGKYNNWDKVDPAELFSCPT 86

Query: 86  EKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININ-SPKTVW 144
           EK+EA P+LK+P FLA E   C++LVLWLDCDKEGENICFEV+ AV+  +N   +P  +W
Sbjct: 87  EKKEAVPRLKIPYFLAKEGAHCDYLVLWLDCDKEGENICFEVIYAVQQGMNKRLNPNDIW 146

Query: 145 RARFSAITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLD 204
           RARFSAIT+KDIK+A+ NL+KPN  EA+SVDARQELDLRIGCAFTR+QTKFFQGKYGDLD
Sbjct: 147 RARFSAITEKDIKSALVNLIKPNENEAKSVDARQELDLRIGCAFTRFQTKFFQGKYGDLD 206

Query: 205 ASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTL-NLNGVAVSVTWSRGHIFDKS 263
            SLISYGPCQTPTLGFCV+RHD+I+TFKP+PYW+L +T+ + +G  + + W+R   FDK 
Sbjct: 207 VSLISYGPCQTPTLGFCVQRHDEIQTFKPDPYWVLQVTVKSSDGQDIILNWTRVRSFDKE 266

Query: 264 TCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERL 323
             N+F   V++    T++ V+S+ K+K++P ALNTVELMRVASSGLGMGPHHAMQIAERL
Sbjct: 267 IANMFLSHVKEYDQATIISVESTEKTKSRPIALNTVELMRVASSGLGMGPHHAMQIAERL 326

Query: 324 YTQGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVGDHP 383
           YTQGY+SYPRTETT YPENFDL+A L+QQ+++PDWGD VR++L+ GI++P+KG +VGDHP
Sbjct: 327 YTQGYISYPRTETTLYPENFDLLAALKQQQNNPDWGDQVRKILTTGINRPKKGCNVGDHP 386

Query: 384 PITPTKLATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLL 443
           PITP K ATR +LDGD WRLYDYI RHFI TL  D  Y     KF +  E+FT     LL
Sbjct: 387 PITPMKHATRNELDGDTWRLYDYITRHFIATLAHDCKYLSTTIKFEIGMEIFTANGHSLL 446

Query: 444 HPGFTGVMTWSAM-KNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGI 502
            PG+T ++TW A+  N+++P F PG+ + IQ +K+VE  T PPDYLTESELISLMEKHGI
Sbjct: 447 DPGYTSILTWQALGSNDNLPRFTPGEKVNIQEIKLVECYTQPPDYLTESELISLMEKHGI 506

Query: 503 GTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRVQ 561
           GTDASIPVHINNIC RNYV V +GR+LVPTSLGIVLVHGYQKID ELV PTMRSA   Q
Sbjct: 507 GTDASIPVHINNICMRNYVNVATGRKLVPTSLGIVLVHGYQKIDPELVLPTMRSAVEEQ 565

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380025214|ref|XP_003696372.1| PREDICTED: DNA topoisomerase 3-beta-1 [Apis florea]

 Score =  777 bits (2006), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 361/539 (66%), Positives = 434/539 (80%), Gaps = 3/539 (0%)

Query: 26  TPLQRMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPT 85
           T  + +NG+CSVHEW+G    + V FKMTSV GH+M LDF  KYNNWDKVDP ELFSCPT
Sbjct: 27  TSRKGLNGSCSVHEWIGQFRSETVNFKMTSVFGHVMTLDFIGKYNNWDKVDPAELFSCPT 86

Query: 86  EKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININ-SPKTVW 144
           EK+EA P+LK+P FLA E   C++LVLWLDCDKEGENICFEV+ AV+  +N   +P  +W
Sbjct: 87  EKKEAVPRLKIPYFLAKEGAHCDYLVLWLDCDKEGENICFEVIYAVQQGMNKRLNPNDIW 146

Query: 145 RARFSAITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLD 204
           RARFSAIT+KDIK+A+ NL+KPN  EA+SVDARQELDLRIGCAFTR+QTKFFQGKYGDLD
Sbjct: 147 RARFSAITEKDIKSALVNLIKPNENEAKSVDARQELDLRIGCAFTRFQTKFFQGKYGDLD 206

Query: 205 ASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTL-NLNGVAVSVTWSRGHIFDKS 263
            SLISYGPCQTPTLGFCV+RHD+I+TFKP+PYW+L +T+ + +G  + + W+R   FDK 
Sbjct: 207 VSLISYGPCQTPTLGFCVQRHDEIQTFKPDPYWVLQVTVKSSDGQDIILNWTRVRSFDKE 266

Query: 264 TCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERL 323
             N+F   V++    T++ V+S+ K+K++P ALNTVELMRVASSGLGMGPHHAMQIAERL
Sbjct: 267 IANMFLSHVKEYDQATIISVESTEKTKSRPIALNTVELMRVASSGLGMGPHHAMQIAERL 326

Query: 324 YTQGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVGDHP 383
           YTQGY+SYPRTETT YPENFDL+A L+QQ+++PDWGD VR++L+ GI++P+KG +VGDHP
Sbjct: 327 YTQGYISYPRTETTLYPENFDLLAALKQQQNNPDWGDQVRKILTTGINRPKKGCNVGDHP 386

Query: 384 PITPTKLATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLL 443
           PITP K ATR +LDGD WRLYDYI RHFI TL  D  Y     KF +  E+FT     LL
Sbjct: 387 PITPMKHATRNELDGDTWRLYDYITRHFIATLAHDCKYLSTTVKFEIGMEIFTANGHSLL 446

Query: 444 HPGFTGVMTWSAM-KNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGI 502
            PG+T ++TW  +  N+++P F PG+ + IQ +K+VE  T PPDYLTESELISLMEKHGI
Sbjct: 447 DPGYTSILTWQTLGSNDNLPRFTPGEKVNIQEIKLVECYTQPPDYLTESELISLMEKHGI 506

Query: 503 GTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRVQ 561
           GTDASIPVHINNIC RNYV V +GR+LVPTSLGIVLVHGYQKID ELV PTMRSA   Q
Sbjct: 507 GTDASIPVHINNICMRNYVNVATGRKLVPTSLGIVLVHGYQKIDPELVLPTMRSAVEEQ 565

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383857261|ref|XP_003704123.1| PREDICTED: DNA topoisomerase 3-beta-1-like [Megachile rotundata]

 Score =  775 bits (2001), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 361/539 (66%), Positives = 432/539 (80%), Gaps = 3/539 (0%)

Query: 26  TPLQRMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPT 85
           T  + +NG+CSVHEWVG    + V FKMTSVCGH+M LDF  KYNNWDKVDP ELFSCPT
Sbjct: 27  TSRKGLNGSCSVHEWVGQFRSETVNFKMTSVCGHVMTLDFIGKYNNWDKVDPAELFSCPT 86

Query: 86  EKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININ-SPKTVW 144
           EK+EA PKLK+P FLA E   C++LVLWLDCDKEGENICFEV+ AV+  +N   +P  +W
Sbjct: 87  EKKEAVPKLKIPYFLAKEGAHCDYLVLWLDCDKEGENICFEVIYAVQQGMNRRLNPNDIW 146

Query: 145 RARFSAITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLD 204
           RARFSAIT+KDIK+A+ NL+KPN  EA+SVDARQELDLRIGCAFTR+QTKFFQGKYGDLD
Sbjct: 147 RARFSAITEKDIKSALANLIKPNENEAKSVDARQELDLRIGCAFTRFQTKFFQGKYGDLD 206

Query: 205 ASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTL-NLNGVAVSVTWSRGHIFDKS 263
           ASLISYGPCQTPTLGFCV+RHD+I+TFKP+PYW+L +T+ + +G  + ++WSR   FDK 
Sbjct: 207 ASLISYGPCQTPTLGFCVQRHDEIQTFKPDPYWVLQVTVKSSDGQDIILSWSRVRSFDKE 266

Query: 264 TCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERL 323
             N+F   +++    TV+ V+SS K+K++P ALNTVELMRVASSGLGMGPHHAMQIAERL
Sbjct: 267 IANMFLSHIKEYDQATVLSVESSEKTKSRPIALNTVELMRVASSGLGMGPHHAMQIAERL 326

Query: 324 YTQGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVGDHP 383
           YTQGY+SYPRTETT YPENFDL A L+QQ+++PDWGD VR++L  GI++P+KG + GDHP
Sbjct: 327 YTQGYISYPRTETTLYPENFDLPAALKQQQNNPDWGDQVRKILMTGINRPKKGHNAGDHP 386

Query: 384 PITPTKLATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLL 443
           PITP K ATR++LDGD+WRLYDYI RHFI TL  D  Y     KF +  E FT     L+
Sbjct: 387 PITPMKHATRSELDGDSWRLYDYITRHFIATLAADCKYLSTTVKFEIGMETFTANGHSLI 446

Query: 444 HPGFTGVMTWSAM-KNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGI 502
            PG+T ++TW  +  N+++P F   + + IQ  K++E  T PPDYLTE+ELISLMEKHGI
Sbjct: 447 DPGYTSILTWQTLGSNDTLPRFTVNEKVNIQETKLLECYTQPPDYLTEAELISLMEKHGI 506

Query: 503 GTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRVQ 561
           GTDASIPVHINNIC RNYV V +GR+LVPTSLGIVLVHGYQKID ELV PTMRSA   Q
Sbjct: 507 GTDASIPVHINNICMRNYVNVAAGRKLVPTSLGIVLVHGYQKIDPELVLPTMRSAVEEQ 565

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307184245|gb|EFN70718.1| DNA topoisomerase 3-beta-1 [Camponotus floridanus]

 Score =  774 bits (1998), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 361/537 (67%), Positives = 430/537 (80%), Gaps = 9/537 (1%)

Query: 31  MNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPTEKREA 90
           +NG+CSVHEWVG    + V FKMTSVCGH+M LDF  KYNNWDKVDP ELFSCPTEK+EA
Sbjct: 32  LNGSCSVHEWVGQFKSETVNFKMTSVCGHVMTLDFIGKYNNWDKVDPAELFSCPTEKKEA 91

Query: 91  TPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRH----QININSPKTVWRA 146
            PKLK+P FLA E   C++L+LWLDCDKEGENICFEV+ AV+     +++IN    +WRA
Sbjct: 92  VPKLKIPYFLAKEGSHCDYLILWLDCDKEGENICFEVINAVQQGMHRKLHIND---IWRA 148

Query: 147 RFSAITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDAS 206
           RFSAIT+KDIK+A+ NL+KPN  EA+SVDARQELDLRIGCAFTRYQTKFFQGKYGDLD S
Sbjct: 149 RFSAITEKDIKSALSNLIKPNENEAKSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDVS 208

Query: 207 LISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNL-NGVAVSVTWSRGHIFDKSTC 265
           LISYGPCQTPTLGFCV+RHD+I+TFKP+PYW+L +T+   +G  + + WSR   FDK   
Sbjct: 209 LISYGPCQTPTLGFCVQRHDEIQTFKPDPYWVLQVTIKCSDGQDIVLNWSRVRSFDKEVA 268

Query: 266 NVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYT 325
           N+F   V++    TVV VQS+ KSK++P ALNTVELMR+ASSGLGMGP HAMQIAERLYT
Sbjct: 269 NMFLSHVKEHDRATVVSVQSTEKSKSRPIALNTVELMRIASSGLGMGPQHAMQIAERLYT 328

Query: 326 QGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVGDHPPI 385
           QGY+SYPRTETT YPENFDL++ L+QQ++SPDWG+ VR++++ GI++P+KG D GDHPPI
Sbjct: 329 QGYISYPRTETTSYPENFDLLSTLKQQQNSPDWGEEVRKIVAAGINRPKKGHDAGDHPPI 388

Query: 386 TPTKLATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHP 445
           TP K ATR +LDGD+WRLYDYI RHFI TL  D  Y     KF +  E FT     LL P
Sbjct: 389 TPMKHATRNELDGDSWRLYDYITRHFIATLARDCKYMSTTIKFEIGIETFTATGHSLLSP 448

Query: 446 GFTGVMTWSAM-KNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGT 504
           G+T ++TW A+  N+++P F   + + IQ  K++E  T PPDYLTE+ELI+LMEKHGIGT
Sbjct: 449 GYTSILTWQALGNNDTLPKFTLDEKVNIQEAKLIECYTQPPDYLTEAELITLMEKHGIGT 508

Query: 505 DASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRVQ 561
           DASIPVHINNIC RNYVTV +GR+LVPTSLGIVLVHGYQKID ELV PTMRSA   Q
Sbjct: 509 DASIPVHINNICIRNYVTVAAGRKLVPTSLGIVLVHGYQKIDPELVLPTMRSAVEEQ 565

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340722711|ref|XP_003399746.1| PREDICTED: DNA topoisomerase 3-beta-1-like [Bombus terrestris]

 Score =  773 bits (1997), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 358/539 (66%), Positives = 432/539 (80%), Gaps = 3/539 (0%)

Query: 26  TPLQRMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPT 85
           T  + +NG+CS+HEW+G    + + FKMTSV GH+M LDF  KYNNWDKVDP ELFSCPT
Sbjct: 27  TSRKGLNGSCSIHEWIGQFRSENINFKMTSVFGHVMTLDFIGKYNNWDKVDPAELFSCPT 86

Query: 86  EKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININ-SPKTVW 144
           EK+EA P+LK+P  LA E   C++L+LWLDCDKEGENICFEV+ AV+  +N   +P  +W
Sbjct: 87  EKKEAVPRLKIPFLLAKEGAHCDYLILWLDCDKEGENICFEVIHAVQQGMNKRLNPNDIW 146

Query: 145 RARFSAITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLD 204
           RARFSAIT+KDIKAA+ NLV+PN  EA+SVDARQE+DLRIGCAFTR+QTKFFQGKYGDLD
Sbjct: 147 RARFSAITEKDIKAALANLVRPNENEAKSVDARQEIDLRIGCAFTRFQTKFFQGKYGDLD 206

Query: 205 ASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNL-NGVAVSVTWSRGHIFDKS 263
            SLISYGPCQTPTLGFCV+RHD+I+TFKP+PYW+L +T+   +G  + ++WSR   FDK 
Sbjct: 207 VSLISYGPCQTPTLGFCVQRHDEIQTFKPDPYWVLQVTVKTSDGQDIILSWSRVRSFDKE 266

Query: 264 TCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERL 323
             N+F   V++    TV+ V+S+ K+K++P ALNTVELMR+ASSGLGMGPHHAMQIAERL
Sbjct: 267 IANMFLSHVKEYDQATVISVESTEKTKSRPIALNTVELMRIASSGLGMGPHHAMQIAERL 326

Query: 324 YTQGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVGDHP 383
           YTQGY+SYPRTETT YPENFDL+A L+QQ+++PDWGD VR++L+ GI++P+KG +VGDHP
Sbjct: 327 YTQGYISYPRTETTLYPENFDLLAALKQQQNNPDWGDQVRKILATGINRPKKGLNVGDHP 386

Query: 384 PITPTKLATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLL 443
           PITP K ATR  LDGD WRLYDYI RHFI TL  D  Y     KF +  EMF       +
Sbjct: 387 PITPMKHATRNDLDGDTWRLYDYITRHFIATLAHDCKYLSTTVKFEIGMEMFMANGHSSI 446

Query: 444 HPGFTGVMTWSAM-KNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGI 502
            PG+T ++TW A+  N+++P F PG+ + IQ +K+VE  T PPDYLTESELISLMEKHGI
Sbjct: 447 DPGYTNILTWQALGSNDTLPKFTPGEKVNIQEMKLVECYTQPPDYLTESELISLMEKHGI 506

Query: 503 GTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRVQ 561
           GTDASIPVHINNIC RNYV VT+GR+LVPTSLGIVLVHGYQKID ELV PTMRSA   Q
Sbjct: 507 GTDASIPVHINNICMRNYVNVTTGRKLVPTSLGIVLVHGYQKIDPELVLPTMRSAVEEQ 565

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350424370|ref|XP_003493773.1| PREDICTED: DNA topoisomerase 3-beta-1-like [Bombus impatiens]

 Score =  773 bits (1996), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 358/539 (66%), Positives = 434/539 (80%), Gaps = 3/539 (0%)

Query: 26  TPLQRMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPT 85
           T  + +NG+CS+HEW+G    + + FKMTSV GH+M LDF  KYNNWDKVDP ELFSCPT
Sbjct: 27  TSRKGLNGSCSIHEWIGQFRSENINFKMTSVFGHVMTLDFIGKYNNWDKVDPAELFSCPT 86

Query: 86  EKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININ-SPKTVW 144
           EK+EA P+LK+P  LA E   C++L+LWLDCDKEGENICFEV+ AV+  +N   +P  +W
Sbjct: 87  EKKEAVPRLKIPFLLAKEGAHCDYLILWLDCDKEGENICFEVIHAVQQGMNRRLNPNDIW 146

Query: 145 RARFSAITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLD 204
           RARFSAIT+KDIKAA+ NLV+PN  EA+SVDARQE+DLRIGCAFTR+QTKFFQGKYGDLD
Sbjct: 147 RARFSAITEKDIKAALANLVRPNENEAKSVDARQEIDLRIGCAFTRFQTKFFQGKYGDLD 206

Query: 205 ASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTL-NLNGVAVSVTWSRGHIFDKS 263
            SLISYGPCQTPTLGFCV+RHD+I+TFKP+PYW+L +T+ + +G  + ++WSR   FDK 
Sbjct: 207 VSLISYGPCQTPTLGFCVQRHDEIQTFKPDPYWVLQVTVKSSDGQDIILSWSRVRSFDKE 266

Query: 264 TCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERL 323
             N+F   V++    TV+ V+S+ K+K++P ALNTVELMR+ASSGLGMGPHHAMQIAERL
Sbjct: 267 IANMFLSHVKEYDQATVISVESTEKTKSRPIALNTVELMRIASSGLGMGPHHAMQIAERL 326

Query: 324 YTQGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVGDHP 383
           YTQGY+SYPRTETT YPENFDL+A L+QQ+++PDWGD VR++L+ GI++P+KG +VGDHP
Sbjct: 327 YTQGYISYPRTETTLYPENFDLLAALKQQQNNPDWGDQVRKILATGINRPKKGLNVGDHP 386

Query: 384 PITPTKLATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLL 443
           PITP K ATR  LDGD WRLYDYI RHFI TL  D  Y     KF +  E+FT      +
Sbjct: 387 PITPMKHATRNDLDGDTWRLYDYITRHFIATLAHDCKYLSTTVKFEIGMEVFTANGHSSI 446

Query: 444 HPGFTGVMTWSAM-KNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGI 502
            PG+T ++TW A+  N+++P F PG+ + IQ +K+VE  T PPDYLTESELISLMEKHGI
Sbjct: 447 DPGYTNILTWQALGSNDTLPRFTPGEKVNIQEMKLVECYTQPPDYLTESELISLMEKHGI 506

Query: 503 GTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRVQ 561
           GTDASIPVHINNIC RNYV VT+GR+LVPTSLGIVLVHGYQKID ELV PTMRSA   Q
Sbjct: 507 GTDASIPVHINNICMRNYVNVTTGRKLVPTSLGIVLVHGYQKIDPELVLPTMRSAVEEQ 565

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307203099|gb|EFN82279.1| DNA topoisomerase 3-beta-1 [Harpegnathos saltator]

 Score =  760 bits (1963), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 356/534 (66%), Positives = 424/534 (79%), Gaps = 3/534 (0%)

Query: 31  MNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPTEKREA 90
           +NG C VHEWV     + V FKMTSVCGH+M LDF  KYNNWDKVDP ELFSCPTEK+EA
Sbjct: 32  LNGTCPVHEWVDQFKYETVTFKMTSVCGHVMTLDFIGKYNNWDKVDPAELFSCPTEKKEA 91

Query: 91  TPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININ-SPKTVWRARFS 149
            PKLK+P  LA E   C++L+LWLDCDKEGENICFEV+ AV+  ++    P  +WRARFS
Sbjct: 92  LPKLKIPYILAKEGSHCDYLILWLDCDKEGENICFEVINAVQQGMHRKLHPNDIWRARFS 151

Query: 150 AITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLIS 209
           AIT+KDIK+A+ NL+KPN  EA+SVDARQELDLRIGCAFTRYQTKFFQGKYGDLD SLIS
Sbjct: 152 AITEKDIKSALENLIKPNENEAKSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDVSLIS 211

Query: 210 YGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNL-NGVAVSVTWSRGHIFDKSTCNVF 268
           YGPCQTPTLGFCV+RHD+I+TFKP+PYW+L +T+   +G  + + WSR   FDK   N+F
Sbjct: 212 YGPCQTPTLGFCVQRHDEIQTFKPDPYWVLQVTIKCADGQDIILNWSRVRSFDKEVANMF 271

Query: 269 FKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGY 328
              V++ +  TVV +QS+ KSK++P ALNTVELMRVASSGLGMGP HAMQIAERLYTQGY
Sbjct: 272 LSHVKEYERATVVSIQSTEKSKSRPIALNTVELMRVASSGLGMGPQHAMQIAERLYTQGY 331

Query: 329 VSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVGDHPPITPT 388
           +SYPRTETT YPENFDL++ L+QQ+++P+WG+ VR++L+ GI++P+KG D GDHPPITP 
Sbjct: 332 ISYPRTETTSYPENFDLLSTLKQQQNNPEWGEDVRKILAAGINRPKKGHDAGDHPPITPM 391

Query: 389 KLATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFT 448
           K ATR +LDGD+WRLYDYI RHFI TL  D  Y     KF +  E+FT     LL  G+T
Sbjct: 392 KHATRNELDGDSWRLYDYITRHFIATLARDCKYLSTTVKFEIGMEIFTATGHSLLDAGYT 451

Query: 449 GVMTWSAM-KNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDAS 507
            ++TW A+  ++++P F   + + IQ  K++E  T PPDYLTE+ELISLMEKHGIGTDAS
Sbjct: 452 SILTWQALGSSDTLPKFTAEEKVNIQEAKLLECYTQPPDYLTEAELISLMEKHGIGTDAS 511

Query: 508 IPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRVQ 561
           IPVHINNIC RNYV VT GRRLVPTSLGIVLVHGYQKID ELV PTMRSA   Q
Sbjct: 512 IPVHINNICIRNYVNVTVGRRLVPTSLGIVLVHGYQKIDPELVLPTMRSAVEEQ 565

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332027377|gb|EGI67460.1| DNA topoisomerase 3-beta-1 [Acromyrmex echinatior]

 Score =  756 bits (1951), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 355/537 (66%), Positives = 426/537 (79%), Gaps = 12/537 (2%)

Query: 31  MNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPTEKREA 90
           +NG+CSVHEWVG    + V FKMTSVCGH+M LDF  KYNNWDKVDP ELFSC TEK+EA
Sbjct: 32  LNGSCSVHEWVGQFRSETVNFKMTSVCGHVMTLDFIGKYNNWDKVDPAELFSCSTEKKEA 91

Query: 91  TPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRH----QININSPKTVWRA 146
            PKLK+P FLA E   C++LVLWLDCDKEGENICFEV+ AV+     +++IN+       
Sbjct: 92  VPKLKIPYFLAKEGAHCDYLVLWLDCDKEGENICFEVINAVQQGMHRKLHINA------T 145

Query: 147 RFSAITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDAS 206
           RFSAIT+KDIK+A+ NL+KPN  EA+SVDARQELDLRIGCAFTRYQTKFFQGKYGDLD S
Sbjct: 146 RFSAITEKDIKSALANLIKPNENEAKSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDVS 205

Query: 207 LISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTL-NLNGVAVSVTWSRGHIFDKSTC 265
           LISYGPCQTPTLGFCV+RHD+I+TFKP+PYW+L +T+ + +G  + ++WSR   FDK   
Sbjct: 206 LISYGPCQTPTLGFCVQRHDEIQTFKPDPYWVLQVTVKSPDGQDIVLSWSRVRSFDKEVA 265

Query: 266 NVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYT 325
           ++F   V++    TVV +QS+ K K++P ALNTVELMRVASSGLGMGP HAMQIAERLYT
Sbjct: 266 SMFLSHVKEYDQATVVSIQSTEKCKSRPIALNTVELMRVASSGLGMGPQHAMQIAERLYT 325

Query: 326 QGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVGDHPPI 385
           QGY+SYPRTETT YPENFDL++ L+QQ++S +WG+ VR++++ GI++P+KG D GDHPPI
Sbjct: 326 QGYISYPRTETTSYPENFDLLSTLKQQQNSSEWGEEVRKIIATGINRPKKGHDAGDHPPI 385

Query: 386 TPTKLATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHP 445
           TP K ATR +LDGD WRLYDYI RHFI TL  D  Y     KF +  E+FT     LL P
Sbjct: 386 TPMKHATRNELDGDLWRLYDYITRHFIATLARDCRYLSTTVKFEIGMEIFTATGHSLLSP 445

Query: 446 GFTGVMTWSAM-KNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGT 504
           G+T ++TW A+  N+++P F   + + IQ  K+VE  T PPDYLTE+ELISLMEKHGIGT
Sbjct: 446 GYTSILTWQALGNNDTLPKFTSDEKVNIQEAKLVECYTQPPDYLTEAELISLMEKHGIGT 505

Query: 505 DASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRVQ 561
           DASIPVHINNIC RNYVTV +GR+L+PTSLGIVLVHGYQKID ELV PTMRSA   Q
Sbjct: 506 DASIPVHINNICIRNYVTVAAGRKLIPTSLGIVLVHGYQKIDPELVLPTMRSAVEEQ 562

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	562
UNIPROTKB|O95985	862	TOP3B "DNA topoisomerase 3-bet	0.944	0.616	0.632	4.7e-183
RGD|1309468	862	Top3b "topoisomerase (DNA) III	0.944	0.616	0.623	2.6e-182
MGI|MGI:1333803	862	Top3b "topoisomerase (DNA) III	0.944	0.616	0.626	1.1e-181
UNIPROTKB|Q5ZK71	862	TOP3B "DNA topoisomerase" [Gal	0.943	0.614	0.618	4.8e-181
UNIPROTKB|E2R770	862	TOP3B "DNA topoisomerase" [Can	0.944	0.616	0.621	6.1e-181
UNIPROTKB|F1RL05	859	TOP3B "DNA topoisomerase" [Sus	0.944	0.618	0.621	7.8e-181
UNIPROTKB|E1BQG8	863	TOP3B "DNA topoisomerase" [Gal	0.943	0.614	0.617	4.3e-180
ZFIN|ZDB-GENE-070705-37	862	top3b "topoisomerase (DNA) III	0.944	0.616	0.612	3e-179
FB|FBgn0026015	875	Top3beta "Topoisomerase 3beta"	0.925	0.594	0.631	5.7e-178
WB|WBGene00012995	869	Y48C3A.14 [Caenorhabditis eleg	0.941	0.608	0.570	1.6e-159

UNIPROTKB|O95985 TOP3B "DNA topoisomerase 3-beta-1" [Homo sapiens (taxid:9606)]

 Score = 1776 (630.2 bits), Expect = 4.7e-183, P = 4.7e-183
 Identities = 339/536 (63%), Positives = 400/536 (74%)

Query:    31 MNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFS-CPTEKRE 89
             +NGACSVHE+ G   G  V FKMTSVCGH+M LDF  KYN WDKVDP ELFS  PTEK+E
Sbjct:    32 LNGACSVHEYTGTFAGQPVRFKMTSVCGHVMTLDFLGKYNKWDKVDPAELFSQAPTEKKE 91

Query:    90 ATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQINI--NSPKTVWRAR 147
             A PKL +  FL  E + C+++VLWLDCDKEGENICFEV++AV   +N      KTV+RAR
Sbjct:    92 ANPKLNMVKFLQVEGRGCDYIVLWLDCDKEGENICFEVLDAVLPVMNKAHGGEKTVFRAR 151

Query:   148 FSAITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASL 207
             FS+ITD DI  AM  L +P+  EA SVDARQELDLRIGCAFTR+QTK+FQGKYGDLD+SL
Sbjct:   152 FSSITDTDICNAMACLGEPDHNEALSVDARQELDLRIGCAFTRFQTKYFQGKYGDLDSSL 211

Query:   208 ISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLN-GVAVSVTWSRGHIFDKSTCN 266
             IS+GPCQTPTLGFCVERHDKI++FKPE YW+L   +N +   ++ + W R  +FD+    
Sbjct:   212 ISFGPCQTPTLGFCVERHDKIQSFKPETYWVLQAKVNTDKDRSLLLDWDRVRVFDREIAQ 271

Query:   267 VFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQ 326
             +F    + EK   V       K+K +P ALNTVE++RVASS LGMGP HAMQ AERLYTQ
Sbjct:   272 MFLNMTKLEKEAQVEATSRKEKAKQRPLALNTVEMLRVASSSLGMGPQHAMQTAERLYTQ 331

Query:   327 GYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVGDHPPIT 386
             GY+SYPRTETT YPENFDL   LRQQ + P W D V+ +L+ GI++PRKG D GDHPPIT
Sbjct:   332 GYISYPRTETTHYPENFDLKGSLRQQANHPYWADTVKRLLAEGINRPRKGHDAGDHPPIT 391

Query:   387 PTKLATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPG 446
             P K AT  +L GDAWRLY+YI RHFI T+  D  Y Q    F +  E+FT   K +L PG
Sbjct:   392 PMKSATEAELGGDAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPELFTCSGKTVLSPG 451

Query:   447 FTGVMTWSAMK-NESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTD 505
             FT VM W ++   ES+P  + GD  P+  VKM+E++T PPDYLTE+ELI+LMEKHGIGTD
Sbjct:   452 FTEVMPWQSVPLEESLPTCQRGDAFPVGEVKMLEKQTNPPDYLTEAELITLMEKHGIGTD 511

Query:   506 ASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRVQ 561
             ASIPVHINNICQRNYVTV SGRRL PT+LGIVLVHGY KID ELV PT+RSA   Q
Sbjct:   512 ASIPVHINNICQRNYVTVESGRRLKPTNLGIVLVHGYYKIDAELVLPTIRSAVEKQ 567

GO:0006265 "DNA topological change" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0003917 "DNA topoisomerase type I activity" evidence=IEA

GO:0000793 "condensed chromosome" evidence=IEA

GO:0007059 "chromosome segregation" evidence=IEA

GO:0003677 "DNA binding" evidence=TAS

GO:0003916 "DNA topoisomerase activity" evidence=TAS

GO:0005634 "nucleus" evidence=TAS

RGD|1309468 Top3b "topoisomerase (DNA) III beta" [Rattus norvegicus (taxid:10116)]

 Score = 1769 (627.8 bits), Expect = 2.6e-182, P = 2.6e-182
 Identities = 334/536 (62%), Positives = 402/536 (75%)

Query:    31 MNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFS-CPTEKRE 89
             +NGACSVH++ G   G  V FKMTSVCGH+M LDF  KYN WDKVDP ELFS  PTEK+E
Sbjct:    32 LNGACSVHKYTGTFAGQPVHFKMTSVCGHVMTLDFLGKYNKWDKVDPAELFSQAPTEKKE 91

Query:    90 ATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQINI--NSPKTVWRAR 147
             A PKL +  FL  E + C+++VLWLDCDKEGENICFEV++AV   +N   N  KTV+RAR
Sbjct:    92 ANPKLNMVKFLQVEGRGCDYVVLWLDCDKEGENICFEVLDAVLPVLNNAHNGEKTVFRAR 151

Query:   148 FSAITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASL 207
             FS+ITD DI  AM  L +P+  EA SVDARQELDLRIGCAFTR+QTK+FQGKYGDLD+SL
Sbjct:   152 FSSITDTDICNAMTRLTEPDHNEALSVDARQELDLRIGCAFTRFQTKYFQGKYGDLDSSL 211

Query:   208 ISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNGV-AVSVTWSRGHIFDKSTCN 266
             IS+GPCQTPTLGFCVERHDKI++FKPE YW+L   ++ +   ++ + W R  +FD+    
Sbjct:   212 ISFGPCQTPTLGFCVERHDKIQSFKPETYWVLQAKVHTDKEESLLLDWDRVRVFDREIAQ 271

Query:   267 VFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQ 326
             +F    + EK   V       K+K +P ALNTVE++RVASS LGMGP HAMQ+AERLYTQ
Sbjct:   272 MFLNMTKLEKEAWVEATSKKEKAKQRPLALNTVEMLRVASSALGMGPQHAMQVAERLYTQ 331

Query:   327 GYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVGDHPPIT 386
             GY+SYPRTETT YPENFDL   LRQQ + P W D V+++L+ GI++PRKG D GDHPPIT
Sbjct:   332 GYISYPRTETTHYPENFDLKGSLRQQANHPYWADSVKQLLAEGINRPRKGHDAGDHPPIT 391

Query:   387 PTKLATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPG 446
             P K AT  +L GDAWRLY+YI RHFI T+  D  Y Q    F +  E FT   K ++ PG
Sbjct:   392 PMKSATEAELGGDAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPEHFTCMGKTVISPG 451

Query:   447 FTGVMTWSAMK-NESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTD 505
             FT +M W ++   ES+P  + GD   +  VKM+E++T+PPDYLTE+ELI+LMEKHGIGTD
Sbjct:   452 FTEIMPWQSVPLEESLPTCQKGDTFTVGEVKMLEKQTSPPDYLTEAELITLMEKHGIGTD 511

Query:   506 ASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRVQ 561
             ASIPVHINNICQRNYVTV +GRRL PT+LGIVLVHGY KID ELV PT+RSA   Q
Sbjct:   512 ASIPVHINNICQRNYVTVENGRRLKPTNLGIVLVHGYHKIDAELVLPTIRSAVEKQ 567

GO:0000793 "condensed chromosome" evidence=IEA;ISO

GO:0003917 "DNA topoisomerase type I activity" evidence=IEA

GO:0006265 "DNA topological change" evidence=IEA

GO:0007059 "chromosome segregation" evidence=IEA;ISO

MGI|MGI:1333803 Top3b "topoisomerase (DNA) III beta" [Mus musculus (taxid:10090)]

 Score = 1763 (625.7 bits), Expect = 1.1e-181, P = 1.1e-181
 Identities = 336/536 (62%), Positives = 401/536 (74%)

Query:    31 MNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFS-CPTEKRE 89
             +NGACSVH++ G   G  V FKMTSVCGH+M LDF  KYN WDKVDP ELFS  PTEK+E
Sbjct:    32 LNGACSVHKYTGTFAGQPVHFKMTSVCGHVMTLDFLGKYNKWDKVDPAELFSQAPTEKKE 91

Query:    90 ATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQINI--NSPKTVWRAR 147
             A PKL +  FL  E + C+++VLWLDCDKEGENICFEV++AV   +N   N  KTV+RAR
Sbjct:    92 ANPKLNMVKFLQVEGRGCDYVVLWLDCDKEGENICFEVLDAVLPVMNNAHNGEKTVFRAR 151

Query:   148 FSAITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASL 207
             FS+ITD DI  AM  L +P+  EA SVDARQELDLRIGCAFTR+QTK+FQGKYGDLD+SL
Sbjct:   152 FSSITDTDICNAMTRLSEPDHNEALSVDARQELDLRIGCAFTRFQTKYFQGKYGDLDSSL 211

Query:   208 ISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNGV-AVSVTWSRGHIFDKSTCN 266
             IS+GPCQTPTLGFCVERHDKI++FKPE YW+L   ++ +   ++ + W R  +FD     
Sbjct:   212 ISFGPCQTPTLGFCVERHDKIQSFKPETYWVLQAKVHTDKEESLLLDWDRVRVFDWEIAQ 271

Query:   267 VFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQ 326
             +F    + EK   V       K+K +P ALNTVE++RVASS LGMGP HAMQIAERLYTQ
Sbjct:   272 MFLNMTKLEKEAWVEATSRKEKAKQRPLALNTVEMLRVASSALGMGPQHAMQIAERLYTQ 331

Query:   327 GYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVGDHPPIT 386
             GY+SYPRTETT YPENFDL   LRQQ + P W D V+++L+ GI++PRKG D GDHPPIT
Sbjct:   332 GYISYPRTETTHYPENFDLKGSLRQQANHPYWADSVKQLLAEGINRPRKGHDAGDHPPIT 391

Query:   387 PTKLATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPG 446
             P K AT  +L GDAWRLY+YI RHFI T+  D  Y Q    F +  E FT   K ++ PG
Sbjct:   392 PMKSATEAELGGDAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPEHFTCMGKTVISPG 451

Query:   447 FTGVMTWSAMK-NESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTD 505
             FT +M W ++   ES+P  + GD   +  VKM+E++T+PPDYLTE+ELI+LMEKHGIGTD
Sbjct:   452 FTEIMPWQSVPLEESLPTCQKGDTFTVGEVKMLEKQTSPPDYLTEAELITLMEKHGIGTD 511

Query:   506 ASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRVQ 561
             ASIPVHINNICQRNYVTV SGRRL PT+LGIVLVHGY KID ELV PT+RSA   Q
Sbjct:   512 ASIPVHINNICQRNYVTVESGRRLKPTNLGIVLVHGYYKIDAELVLPTIRSAVEKQ 567

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000793 "condensed chromosome" evidence=IDA

GO:0003677 "DNA binding" evidence=IEA

GO:0003916 "DNA topoisomerase activity" evidence=IEA

GO:0003917 "DNA topoisomerase type I activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005694 "chromosome" evidence=IEA

GO:0006265 "DNA topological change" evidence=IEA

GO:0007059 "chromosome segregation" evidence=IMP

GO:0016853 "isomerase activity" evidence=IEA

UNIPROTKB|Q5ZK71 TOP3B "DNA topoisomerase" [Gallus gallus (taxid:9031)]

 Score = 1757 (623.6 bits), Expect = 4.8e-181, P = 4.8e-181
 Identities = 332/537 (61%), Positives = 401/537 (74%)

Query:    31 MNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFS-CPTEKRE 89
             +NG CSVHE+ G   G    FKMTSVCGH+M LDF  KYN+WDKVDP ELFS  PTEK+E
Sbjct:    32 LNGVCSVHEYTGSFIGQSAHFKMTSVCGHVMTLDFIGKYNSWDKVDPAELFSKAPTEKKE 91

Query:    90 ATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKT---VWRA 146
             A PKL +  FL  E + C+ +VLWLDCDKEGENICFEV++AV   +N  SP T   ++RA
Sbjct:    92 ANPKLTMVKFLQVEGRGCDSIVLWLDCDKEGENICFEVLDAVLPVMN-KSPSTERMIYRA 150

Query:   147 RFSAITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDAS 206
             +FS+ITD DI  AM +L +PN+ EA SVDARQELDLRIGCAFTR+QTK+FQGKYG+LD+S
Sbjct:   151 KFSSITDTDICNAMNHLGEPNLNEALSVDARQELDLRIGCAFTRFQTKYFQGKYGNLDSS 210

Query:   207 LISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNGVA-VSVTWSRGHIFDKSTC 265
             LIS+GPCQTPTLGFCVERHDKI++FKPE YW+L   +N    + +++ W R  +FD+   
Sbjct:   211 LISFGPCQTPTLGFCVERHDKIQSFKPETYWVLQAKVNPEKESSLTLDWDRVRVFDREIA 270

Query:   266 NVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYT 325
              +F    +  K   V  V    K K +P ALNTVE++RVAS+ LGMGP HAMQIAERLYT
Sbjct:   271 QMFLNITKMAKEAKVESVSKKEKVKQRPLALNTVEMLRVASAALGMGPQHAMQIAERLYT 330

Query:   326 QGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVGDHPPI 385
             QGY+SYPRTETT YPENFDL   LRQQ ++P W + V+ +LS GI++PRKG D GDHPPI
Sbjct:   331 QGYISYPRTETTHYPENFDLKGCLRQQANNPYWAETVKALLSEGINRPRKGHDAGDHPPI 390

Query:   386 TPTKLATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHP 445
             TP K AT  +L GD+WRLY+YI RHFI T+  D  Y Q    FS+  E F    K +  P
Sbjct:   391 TPMKAATEVELGGDSWRLYEYITRHFIATVSADCKYLQTNISFSIGPERFNCVGKVVTSP 450

Query:   446 GFTGVMTWSAMK-NESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGT 504
             GFT +M W ++   ES+P  + GDL P+  +K++E +T+PPDYLTE+ELI+LMEKHGIGT
Sbjct:   451 GFTEIMPWHSIALEESLPSCEKGDLFPVGEIKLLEMQTSPPDYLTEAELITLMEKHGIGT 510

Query:   505 DASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRVQ 561
             DASIPVHINNICQRNYVTV SGRRL PT+LGIVLVHGY KID ELV PT+RSA   Q
Sbjct:   511 DASIPVHINNICQRNYVTVESGRRLKPTNLGIVLVHGYYKIDAELVLPTIRSAVEKQ 567

GO:0005694 "chromosome" evidence=IEA

GO:0006265 "DNA topological change" evidence=IEA

GO:0003917 "DNA topoisomerase type I activity" evidence=IEA

UNIPROTKB|E2R770 TOP3B "DNA topoisomerase" [Canis lupus familiaris (taxid:9615)]

 Score = 1756 (623.2 bits), Expect = 6.1e-181, P = 6.1e-181
 Identities = 333/536 (62%), Positives = 400/536 (74%)

Query:    31 MNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFS-CPTEKRE 89
             +NG CSVHE+ G   G  V FKMTSVCGH+M LDF  KYN WDKVDP ELFS  PTEK+E
Sbjct:    32 LNGTCSVHEYSGTFAGQPVRFKMTSVCGHVMTLDFLGKYNKWDKVDPAELFSQAPTEKKE 91

Query:    90 ATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQINI--NSPKTVWRAR 147
             A PKL +  FL  E K C+++VLWLDCDKEGENICFEV++AV   +N   +  KTV+RAR
Sbjct:    92 ANPKLNMVKFLQVEGKGCDYIVLWLDCDKEGENICFEVLDAVLPVMNPTHSGEKTVFRAR 151

Query:   148 FSAITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASL 207
             FS+ITD DI AAM  L +P+  EA SVDARQELDLRIGCAFTR+QTK+FQGKYG+LD+SL
Sbjct:   152 FSSITDTDICAAMARLGEPDHNEALSVDARQELDLRIGCAFTRFQTKYFQGKYGNLDSSL 211

Query:   208 ISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLN-GVAVSVTWSRGHIFDKSTCN 266
             IS+GPCQTPTLGFCVERHDKI++FKPE YW+L   +N +   ++ + W R  +FD+    
Sbjct:   212 ISFGPCQTPTLGFCVERHDKIQSFKPETYWVLQAKVNADKDRSLLLDWDRVRVFDREIAQ 271

Query:   267 VFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQ 326
             +F    + EK   V       K+K +P ALNTVE++RVASS LGMGP HAMQ AERLYTQ
Sbjct:   272 MFLNMTKLEKEAQVEATSRKEKAKQRPLALNTVEMLRVASSSLGMGPQHAMQTAERLYTQ 331

Query:   327 GYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVGDHPPIT 386
             GY+SYPRTETT YPENFDL   LRQQ + P W D V+ +L+ GI++PRKG D GDHPPIT
Sbjct:   332 GYISYPRTETTHYPENFDLKGPLRQQANHPYWADTVKRLLAEGINRPRKGHDAGDHPPIT 391

Query:   387 PTKLATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPG 446
             P + AT  +L  +AWRLY+YI RHFI T+  D  Y Q    F +  E FT   K ++ PG
Sbjct:   392 PMRSATEAELGSEAWRLYEYITRHFIATVSYDCKYLQSTISFRIGPEHFTCTGKTVISPG 451

Query:   447 FTGVMTWSAMK-NESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTD 505
             FT +M W ++   ES+P  + GD  P+  +KM+E++T+PPDYLTE+ELI+LMEKHGIGTD
Sbjct:   452 FTEIMPWQSVPLEESLPTCQRGDCFPVSEMKMLEKQTSPPDYLTEAELITLMEKHGIGTD 511

Query:   506 ASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRVQ 561
             ASIPVHINNICQRNYVTV SGRRL PT+LGIVLVHGY KID ELV PT+RSA   Q
Sbjct:   512 ASIPVHINNICQRNYVTVESGRRLKPTNLGIVLVHGYYKIDAELVLPTIRSAVEKQ 567

GO:0007059 "chromosome segregation" evidence=IEA

GO:0000793 "condensed chromosome" evidence=IEA

GO:0003917 "DNA topoisomerase type I activity" evidence=IEA

GO:0006265 "DNA topological change" evidence=IEA

UNIPROTKB|F1RL05 TOP3B "DNA topoisomerase" [Sus scrofa (taxid:9823)]

 Score = 1755 (622.8 bits), Expect = 7.8e-181, P = 7.8e-181
 Identities = 333/536 (62%), Positives = 400/536 (74%)

Query:    31 MNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFS-CPTEKRE 89
             +NG CSVHE+ G   G  V FKMTSVCGH+M LDF  KYN WDKVDP ELFS  PTEK+E
Sbjct:    32 LNGTCSVHEYTGTFAGQPVHFKMTSVCGHVMTLDFLGKYNKWDKVDPAELFSQAPTEKKE 91

Query:    90 ATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQINI--NSPKTVWRAR 147
             A PKL +  FL  E K C+++VLWLDCDKEGENICFEV++AV   +N    S KTV+RAR
Sbjct:    92 ANPKLNMVKFLQVEGKGCDYIVLWLDCDKEGENICFEVLDAVLPVMNQAHGSEKTVFRAR 151

Query:   148 FSAITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASL 207
             FS+ITD DI  AM +L +P+  EA SVDARQELDLRIGCAFTR+QTK+FQGKYGDLD+SL
Sbjct:   152 FSSITDTDICNAMAHLGEPDHNEALSVDARQELDLRIGCAFTRFQTKYFQGKYGDLDSSL 211

Query:   208 ISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLN-GVAVSVTWSRGHIFDKSTCN 266
             IS+GPCQTPTLGFCVERHDKI++FKPE YW+L   +N +   ++ + W R  +FD+    
Sbjct:   212 ISFGPCQTPTLGFCVERHDKIQSFKPETYWVLQAKVNTDQDRSLLLDWDRVRVFDREIAQ 271

Query:   267 VFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQ 326
             +F    + EK   V       K+K +P ALNTVE++RVASS LGMGP HAMQ AERLYTQ
Sbjct:   272 MFLNMTKPEKEAQVEATSKKEKTKQRPLALNTVEMLRVASSALGMGPQHAMQTAERLYTQ 331

Query:   327 GYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVGDHPPIT 386
             GY+SYPRTETT YPE+FDL   LRQQ + P W D V+++L+ GI++PRKG D GDHPPIT
Sbjct:   332 GYISYPRTETTHYPESFDLKGPLRQQANHPYWADTVKQLLAEGINRPRKGHDAGDHPPIT 391

Query:   387 PTKLATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPG 446
             P + AT  +L G+AWRLY+YI RHFI T+  D  Y Q    F +  E FT   K ++ PG
Sbjct:   392 PMRSATEAELGGEAWRLYEYITRHFIATVSHDCRYLQSTISFRIGPERFTCTGKTVISPG 451

Query:   447 FTGVMTWSAMK-NESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTD 505
             FT +M W ++   ES+P  + GD   +  VKM+E++T+PPDYLTE+ELI+LMEKHGIGTD
Sbjct:   452 FTEIMPWQSVPLEESLPTCQKGDTFAVGEVKMLEKQTSPPDYLTEAELITLMEKHGIGTD 511

Query:   506 ASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRVQ 561
             ASIPVHINNICQRNYV V SGRRL PT+LGIVLVHGY KID ELV PT+RSA   Q
Sbjct:   512 ASIPVHINNICQRNYVVVESGRRLKPTNLGIVLVHGYYKIDAELVLPTIRSAVEKQ 567

GO:0007059 "chromosome segregation" evidence=IEA

GO:0000793 "condensed chromosome" evidence=IEA

GO:0003917 "DNA topoisomerase type I activity" evidence=IEA

GO:0006265 "DNA topological change" evidence=IEA

UNIPROTKB|E1BQG8 TOP3B "DNA topoisomerase" [Gallus gallus (taxid:9031)]

 Score = 1748 (620.4 bits), Expect = 4.3e-180, P = 4.3e-180
 Identities = 332/538 (61%), Positives = 401/538 (74%)

Query:    31 MNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFS-CPTEKRE 89
             +NG CSVHE+ G   G    FKMTSVCGH+M LDF  KYN+WDKVDP ELFS  PTEK+E
Sbjct:    32 LNGVCSVHEYTGSFIGQSAHFKMTSVCGHVMTLDFIGKYNSWDKVDPAELFSKAPTEKKE 91

Query:    90 ATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKT---VWRA 146
             A PKL +  FL  E + C+ +VLWLDCDKEGENICFEV++AV   +N  SP T   ++RA
Sbjct:    92 ANPKLTMVKFLQVEGRGCDSIVLWLDCDKEGENICFEVLDAVLPVMN-KSPSTERMIYRA 150

Query:   147 RFSAITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDAS 206
             +FS+ITD DI  AM +L +PN+ EA SVDARQELDLRIGCAFTR+QTK+FQGKYG+LD+S
Sbjct:   151 KFSSITDTDICNAMNHLGEPNLNEALSVDARQELDLRIGCAFTRFQTKYFQGKYGNLDSS 210

Query:   207 LISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNGVA-VSVTWSRGHIFDKSTC 265
             LIS+GPCQTPTLGFCVERHDKI++FKPE YW+L   +N    + +++ W R  +FD+   
Sbjct:   211 LISFGPCQTPTLGFCVERHDKIQSFKPETYWVLQAKVNPEKESSLTLDWDRVRVFDREIA 270

Query:   266 NVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYT 325
              +F    +  K   V  V    K K +P ALNTVE++RVAS+ LGMGP HAMQIAERLYT
Sbjct:   271 QMFLNITKMAKEAKVESVSKKEKVKQRPLALNTVEMLRVASAALGMGPQHAMQIAERLYT 330

Query:   326 QGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVGDHPPI 385
             QGY+SYPRTETT YPENFDL   LRQQ ++P W + V+ +LS GI++PRKG D GDHPPI
Sbjct:   331 QGYISYPRTETTHYPENFDLKGCLRQQANNPYWAETVKALLSEGINRPRKGHDAGDHPPI 390

Query:   386 TPTKLATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHP 445
             TP K AT  +L GD+WRLY+YI RHFI T+  D  Y Q    FS+  E F    K +  P
Sbjct:   391 TPMKAATEVELGGDSWRLYEYITRHFIATVSADCKYLQTNISFSIGPERFNCVGKVVTSP 450

Query:   446 GFTGVMTWSAMK-NESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGT 504
             GFT +M W ++   ES+P  + GDL P+  +K++E +T+PPDYLTE+ELI+LMEKHGIGT
Sbjct:   451 GFTEIMPWHSIALEESLPSCEKGDLFPVGEIKLLEMQTSPPDYLTEAELITLMEKHGIGT 510

Query:   505 DASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKI-DRELVEPTMRSAYRVQ 561
             DASIPVHINNICQRNYVTV SGRRL PT+LGIVLVHGY KI D ELV PT+RSA   Q
Sbjct:   511 DASIPVHINNICQRNYVTVESGRRLKPTNLGIVLVHGYYKIVDAELVLPTIRSAVEKQ 568

GO:0006265 "DNA topological change" evidence=IEA

GO:0000793 "condensed chromosome" evidence=IEA

GO:0007059 "chromosome segregation" evidence=IEA

GO:0003917 "DNA topoisomerase type I activity" evidence=IEA

ZFIN|ZDB-GENE-070705-37 top3b "topoisomerase (DNA) III beta" [Danio rerio (taxid:7955)]

 Score = 1740 (617.6 bits), Expect = 3.0e-179, P = 3.0e-179
 Identities = 329/537 (61%), Positives = 402/537 (74%)

Query:    31 MNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFS-CPTEKRE 89
             +NGACSVHE++G   G  V FKMTSVCGH+M LDF  KYNNWDKVDP ELFS  PTEK+E
Sbjct:    32 LNGACSVHEYMGSFTGQNVRFKMTSVCGHVMSLDFIGKYNNWDKVDPAELFSKAPTEKKE 91

Query:    90 ATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQIN--INSPKTVWRAR 147
             A PKL +  FL  EAK C+++VLWLDCDKEGENICFEV++A++  +N    + +TV+RA+
Sbjct:    92 ANPKLNMVKFLQVEAKGCDYVVLWLDCDKEGENICFEVLDAIQPVMNKPYGNERTVYRAK 151

Query:   148 FSAITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASL 207
             FS+ITD DI  AM  L +PN  EA SVDARQELDLRIGCAFTR+QTK+FQGKYG+LD+SL
Sbjct:   152 FSSITDTDICNAMNRLGEPNKNEALSVDARQELDLRIGCAFTRFQTKYFQGKYGNLDSSL 211

Query:   208 ISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVT--WSRGHIFDKSTC 265
             IS+GPCQTPTLGFCVERHDKI++FKPE YW++   +   G    +T  W R  +FD+   
Sbjct:   212 ISFGPCQTPTLGFCVERHDKIQSFKPEAYWVVQAKVANFGKDSPLTLDWDRVRVFDRDIG 271

Query:   266 NVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYT 325
              +F    +  K   V  V    K+K +P ALNTVE++RVASS LGMGP H MQIAERLYT
Sbjct:   272 QMFVNMAKTAKEARVDSVTKKEKAKQRPLALNTVEMLRVASSALGMGPQHTMQIAERLYT 331

Query:   326 QGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVGDHPPI 385
             QGY+SYPRTETT YPENFDL   L+QQ +S  WG+ V+ +LS GI++PRKG D GDHPPI
Sbjct:   332 QGYISYPRTETTHYPENFDLKGTLKQQANSTFWGETVKALLSEGINRPRKGADAGDHPPI 391

Query:   386 TPTKLATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHP 445
             TP + A+  +L  D WRLYDYI RHFI T+  D  Y Q    FS+A E FT   K L+  
Sbjct:   392 TPMRAASENELGSDGWRLYDYITRHFIATVSPDCKYLQTTISFSIATEGFTCSGKTLISA 451

Query:   446 GFTGVMTWSAM-KNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGT 504
             G+T VM W  + + E++P  + G++  +  +K++E++T PPDYLTE+ELI+LMEKHGIGT
Sbjct:   452 GYTEVMPWQGIAQEEALPVCERGEMFTVDEIKLLEKQTNPPDYLTEAELITLMEKHGIGT 511

Query:   505 DASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRVQ 561
             DASIPVHINNICQRNYVTV SGR+L PT+LGIVLVHGY KID +LV PT+RSA   Q
Sbjct:   512 DASIPVHINNICQRNYVTVESGRKLKPTNLGIVLVHGYYKIDADLVLPTIRSAVEKQ 568

GO:0003677 "DNA binding" evidence=IEA

GO:0003916 "DNA topoisomerase activity" evidence=IEA

GO:0005694 "chromosome" evidence=IEA

GO:0006265 "DNA topological change" evidence=IEA

GO:0003917 "DNA topoisomerase type I activity" evidence=IEA

GO:0016853 "isomerase activity" evidence=IEA

FB|FBgn0026015 Top3beta "Topoisomerase 3beta" [Drosophila melanogaster (taxid:7227)]

 Score = 1728 (613.3 bits), Expect = 5.7e-178, P = 5.7e-178
 Identities = 334/529 (63%), Positives = 396/529 (74%)

Query:    32 NGACSVHEWVGPLFGD-LVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPTEKREA 90
             NG CS HEW G    +  V F+MTSVCGH+M LDF  KYN WDKVDP++LF C TEK+E 
Sbjct:    34 NG-CSTHEWTGNFRNEGSVHFRMTSVCGHVMSLDFNKKYNCWDKVDPIQLFGCATEKKET 92

Query:    91 TPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQIN-INSPKTVWRARFS 149
              PK  +  FLA+EA+ C++LVLWLDCDKEGENICFEVM+AV+H IN + S +  +RA FS
Sbjct:    93 NPKQNMRKFLAHEARGCDYLVLWLDCDKEGENICFEVMDAVKHVINNVYSDQVTYRAHFS 152

Query:   150 AITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLIS 209
             AIT+KDIK AM  L  PN  EA+SVDARQELDLRIGCAFTR+QTKFFQ +YGDLD+SLIS
Sbjct:   153 AITEKDIKKAMETLGHPNENEAKSVDARQELDLRIGCAFTRFQTKFFQDRYGDLDSSLIS 212

Query:   210 YGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNGVA-VSVTWSRGHIFDKSTCNVF 268
             YGPCQTPTLGFCV+RHD I+TFKPE +W L L   L G   V++ W+RG +F K    + 
Sbjct:   213 YGPCQTPTLGFCVKRHDDIQTFKPESFWHLQL---LAGQPEVTLEWARGRVFKKDIAIML 269

Query:   269 FKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGY 328
                V++ K  TV  V S    K+KPQALNTVELMR+ SSGLG+GP  AMQIAERLYTQGY
Sbjct:   270 LNRVKEHKKATVESVASKEAYKSKPQALNTVELMRICSSGLGIGPFQAMQIAERLYTQGY 329

Query:   329 VSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVGDHPPITPT 388
             +SYPRTET QYP NFDL AVL   + S D+G+  R +L + I  PRKGKD GDHPPITP 
Sbjct:   330 ISYPRTETNQYPTNFDLPAVLHVLKPSADFGEEARSILGD-IQTPRKGKDAGDHPPITPM 388

Query:   389 KLATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFT 448
             KL  R+  D D WR+Y++I RHF+GT+  DL Y    AK SV  E F+  A  L+  GFT
Sbjct:   389 KLGNRSDFDRDTWRVYEFICRHFMGTVSRDLKYRVTTAKLSVGMETFSCTASVLIDAGFT 448

Query:   449 GVMTWSAM-KNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDAS 507
              VMTWSA  K+E  P F  G  + I  V+++E +T PPDYLTESELI+LME+HGIGTDAS
Sbjct:   449 KVMTWSAFGKDEPQPPFVQGTQVAINDVRLIESQTGPPDYLTESELITLMEEHGIGTDAS 508

Query:   508 IPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRS 556
             IPVHINNICQRNYV + +GR+L+PT+LGIVLVHGYQKID ELV PTMR+
Sbjct:   509 IPVHINNICQRNYVHIENGRKLMPTTLGIVLVHGYQKIDPELVLPTMRT 557

GO:0003917 "DNA topoisomerase type I activity" evidence=ISS;NAS

GO:0003916 "DNA topoisomerase activity" evidence=IDA;NAS

GO:0004520 "endodeoxyribonuclease activity" evidence=IDA

GO:0000737 "DNA catabolic process, endonucleolytic" evidence=IDA

GO:0006265 "DNA topological change" evidence=IEA

GO:0005694 "chromosome" evidence=IEA

WB|WBGene00012995 Y48C3A.14 [Caenorhabditis elegans (taxid:6239)]

 Score = 1554 (552.1 bits), Expect = 1.6e-159, P = 1.6e-159
 Identities = 307/538 (57%), Positives = 376/538 (69%)

Query:    32 NGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPTEKREAT 91
             NG CSV E+ G   G    FK+TS CGH+M LDF  K+NNW++VDP EL+S PT++ EA 
Sbjct:    34 NGVCSVSEYDGQFNGRAARFKVTSTCGHVMSLDFPPKFNNWERVDPAELYSAPTQRIEAN 93

Query:    92 PKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSP---KTVWRARF 148
             PK+K+  FLA+EAK+ +FLVLWLDCDKEGENICFEV++AV+  +  N       V+RA F
Sbjct:    94 PKMKMNEFLASEAKNADFLVLWLDCDKEGENICFEVIDAVKCAMFKNRQDFMSDVYRAHF 153

Query:   149 SAITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLI 208
             SAIT+KDIKAAM NL +P+   + SVDARQELDLRIGC+FTR+QTKFFQGKYGDLD+++I
Sbjct:   154 SAITEKDIKAAMRNLGRPDQNMSHSVDARQELDLRIGCSFTRFQTKFFQGKYGDLDSNVI 213

Query:   209 SYGPCQTPTLGFCVERHDKIRTFKPEPYWLL--DLTLNLNGVAVSVTWSRGHIFDKSTCN 266
             SYGPCQTPTLGFCV RHD+I  FKPE YW+L  + T + +G   S  W RG IFD     
Sbjct:   214 SYGPCQTPTLGFCVTRHDQIVQFKPEQYWVLKTNFTTSDDGQIFSPEWQRGRIFDAEVAR 273

Query:   267 VFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQ 326
             VF   ++K     V+DV      K +P ALNTVELMRVASS LGM P   M +AE LYTQ
Sbjct:   274 VFVDRIKKCHTGLVLDVSKKEARKERPCALNTVELMRVASSSLGMSPSTTMHVAEALYTQ 333

Query:   327 GYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVGDHPPIT 386
             GY+SYPRTETT Y  NFDL   L+       WG  V +VL++GI +P+ G D GDHPPIT
Sbjct:   334 GYISYPRTETTAYSANFDLTGTLKILAGDRKWGSVVSQVLADGIKRPKSGVDKGDHPPIT 393

Query:   387 PTKLATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPG 446
             P +      L GD  R+Y+Y+ +HF+ TL    VY     K S  DE FT++ K ++ PG
Sbjct:   394 PMR-PNHGGLSGDMSRIYEYVSQHFVATLMKQCVYEVTTVKMSCGDEQFTLQGKNVVEPG 452

Query:   447 FTGVMTWSAMKNE-SIPDF--KPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIG 503
             FT VM W +++ E S+P    + G  I +Q+ ++  R+TTPP YLTE+ELI+LMEKHGIG
Sbjct:   453 FTAVMPWLSVEEECSVPKSLQQIGAKIELQNAEIQARETTPPGYLTEAELITLMEKHGIG 512

Query:   504 TDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRVQ 561
             TDASIPVHIN I QRNYVTV SGRRLVPT LG  LV GY K+D ELV PTMR+    Q
Sbjct:   513 TDASIPVHINTITQRNYVTVESGRRLVPTRLGQCLVRGYWKVDPELVLPTMRAELEEQ 570

GO:0003677 "DNA binding" evidence=IEA

GO:0003917 "DNA topoisomerase type I activity" evidence=IEA

GO:0005694 "chromosome" evidence=IEA

GO:0006265 "DNA topological change" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0008168 "methyltransferase activity" evidence=IEA

GO:0032259 "methylation" evidence=IEA

GO:0003916 "DNA topoisomerase activity" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q8T2T7	TOP3_DICDI	5, ., 9, 9, ., 1, ., 2	0.3506	0.8861	0.6014	yes	N/A
O28469	TOP1_ARCFU	5, ., 9, 9, ., 1, ., 2	0.3161	0.7900	0.6696	yes	N/A
O96651	TOP3B_DROME	5, ., 9, 9, ., 1, ., 2	0.6299	0.9234	0.5931	yes	N/A
Q9HM08	TOP1_THEAC	5, ., 9, 9, ., 1, ., 2	0.3009	0.8523	0.6220	yes	N/A
O60126	TOP3_SCHPO	5, ., 9, 9, ., 1, ., 2	0.3256	0.9003	0.8135	yes	N/A
Q9Z321	TOP3B_MOUSE	5, ., 9, 9, ., 1, ., 2	0.6268	0.9448	0.6160	yes	N/A
O95985	TOP3B_HUMAN	5, ., 9, 9, ., 1, ., 2	0.6273	0.9555	0.6229	yes	N/A
P13099	TOP3_YEAST	5, ., 9, 9, ., 1, ., 2	0.3258	0.8825	0.7560	yes	N/A

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
4th Layer	5.99.1.2	0.914
3rd Layer	5.99.1	0.921

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	562
COG0550	570	COG0550, TopA, Topoisomerase IA [DNA replication,	1e-125
PRK07219	822	PRK07219, PRK07219, DNA topoisomerase I; Validated	1e-123
cd00186	381	cd00186, TOP1Ac, DNA Topoisomerase, subtype IA; DN	1e-121
pfam01131	365	pfam01131, Topoisom_bac, DNA topoisomerase	1e-105
PRK07220	740	PRK07220, PRK07220, DNA topoisomerase I; Validated	6e-95
smart00437	259	smart00437, TOP1Ac, Bacterial DNA topoisomerase I	6e-82
PRK14973	936	PRK14973, PRK14973, DNA topoisomerase I; Provision	1e-78
PRK05776	670	PRK05776, PRK05776, DNA topoisomerase I; Provision	1e-58
TIGR01057	618	TIGR01057, topA_arch, DNA topoisomerase I, archaea	7e-58
PRK07726	658	PRK07726, PRK07726, DNA topoisomerase III; Provisi	2e-45
TIGR01056	660	TIGR01056, topB, DNA topoisomerase III, bacteria a	6e-41
TIGR01051	610	TIGR01051, topA_bact, DNA topoisomerase I, bacteri	3e-39
cd03362	151	cd03362, TOPRIM_TopoIA_TopoIII, TOPRIM_TopoIA_Topo	3e-36
PRK05582	650	PRK05582, PRK05582, DNA topoisomerase I; Validated	8e-34
cd01028	142	cd01028, TOPRIM_TopoIA, TOPRIM_TopoIA: topoisomera	4e-33
smart00436	89	smart00436, TOP1Bc, Bacterial DNA topoisomeraes I	3e-29
TIGR01054	1171	TIGR01054, rgy, reverse gyrase	2e-28
PRK08173	862	PRK08173, PRK08173, DNA topoisomerase III; Validat	4e-28
COG1110	1187	COG1110, COG1110, Reverse gyrase [DNA replication,	2e-27
PRK07561	859	PRK07561, PRK07561, DNA topoisomerase I subunit om	1e-26
PRK06599	675	PRK06599, PRK06599, DNA topoisomerase I; Validated	2e-26
PRK08780	780	PRK08780, PRK08780, DNA topoisomerase I; Provision	1e-23
PRK09401	1176	PRK09401, PRK09401, reverse gyrase; Reviewed	4e-23
PRK14724	987	PRK14724, PRK14724, DNA topoisomerase III; Provisi	8e-22
PRK06319	860	PRK06319, PRK06319, DNA topoisomerase I/SWI domain	1e-16
PRK14701	1638	PRK14701, PRK14701, reverse gyrase; Provisional	9e-10
PTZ00407	805	PTZ00407, PTZ00407, DNA topoisomerase IA; Provisio	6e-09
PRK14701	1638	PRK14701, PRK14701, reverse gyrase; Provisional	8e-06
cd03363	123	cd03363, TOPRIM_TopoIA_TopoI, TOPRIM_TopoIA_TopoI:	6e-05
smart00493	75	smart00493, TOPRIM, topoisomerases, DnaG-type prim	4e-04
pfam01751	86	pfam01751, Toprim, Toprim domain	0.003

>gnl|CDD|223624 COG0550, TopA, Topoisomerase IA [DNA replication, recombination, and repair]

 Score =  379 bits (976), Expect = e-125
 Identities = 148/518 (28%), Positives = 220/518 (42%), Gaps = 32/518 (6%)

Query: 51  FKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPTEKREATPKLKLP--AFLANEAKDCE 108
           + +T+  GH+  L F  +Y  W  VD          K    P  K      L   AK  +
Sbjct: 23  YVVTASVGHLRDLPFPEEYKGWVDVDLPIFE----PKYIIKPGKKKKVVKKLKKLAKKAD 78

Query: 109 FLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNLVKPNI 168
            + L  D D+EGE I + ++E     + + +P  V R  FS IT K I +A  N  + ++
Sbjct: 79  EVYLATDPDREGEAIGWHILE----VLKLKNPSKVKRVVFSEITKKAILSAFKNPREIDM 134

Query: 169 FEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKI 228
               +  AR+ LD  +G   +R   K  +         ++S G  Q+P L   VER  +I
Sbjct: 135 NLVDAQLARRILDRLVGYNLSRLLWKKLKRG-------VLSAGRVQSPALRLVVEREREI 187

Query: 229 RTFKPEPYWLLDLTLNLNGVAVSVTWSR---GHIFDKSTCNVFFKAVEKEKH--VTVVDV 283
             F PE YW +       G   S   +             +   + V K K     VV V
Sbjct: 188 EAFVPEEYWEIKAIFEKGGGEFSARLTEIEGKKEGRLKDKDEAEEIVNKLKGKPAKVVSV 247

Query: 284 QSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLY-TQGYVSYPRTETTQYPEN 342
           +   K ++ P    T  L + AS  LG      M IA++LY   G ++YPRT++T+  E 
Sbjct: 248 EKKPKKRSPPPPFTTSTLQQEASRKLGFSAKKTMDIAQKLYEGHGLITYPRTDSTRLSEE 307

Query: 343 FDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGK-DVGDHPPITPTKLATRTQL-DGDA 400
               A L     +  +G     +       P KGK     H  I PT   T   L   D 
Sbjct: 308 ALAEARLYILAIA--YGKEYLPLKPR--RYPSKGKKAQEAHEAIRPTDFETPESLKAYDE 363

Query: 401 WRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNES 460
            +LYD I R F+ +   D +Y +      VA E F    K L   G+  V      + E 
Sbjct: 364 LKLYDLIWRRFLASQMPDAIYEKTTVTLEVAGEKFKASGKVLKFDGWLKVYGEDKDEEED 423

Query: 461 I--PDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQR 518
              P+ K GD + ++ +++ E  T PP   TE+ L+  MEK GIGT ++    I  + +R
Sbjct: 424 KELPELKEGDELKVEKLEVEEHFTKPPPRYTEASLVKAMEKLGIGTPSTYASIIETLQKR 483

Query: 519 NYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRS 556
            YV    G+RLVPT LG  ++   ++   ELV+P   +
Sbjct: 484 GYVEK-KGKRLVPTELGEAVIELLEEYFPELVDPDFTA 520

Length = 570

>gnl|CDD|235971 PRK07219, PRK07219, DNA topoisomerase I; Validated

 Score =  382 bits (984), Expect = e-123
 Identities = 167/532 (31%), Positives = 263/532 (49%), Gaps = 21/532 (3%)

Query: 30  RMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPTEKRE 89
           R+NG    +E+          + +  + GHI+ +DF  +Y +W  VDP EL      K+ 
Sbjct: 28  RVNGV-PYYEFER----KGEKWIVIGLSGHIVTVDFPEEYGDWRDVDPAELIDADPVKKI 82

Query: 90  ATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFS 149
              K      L   AKD + +++  D D+EGE I  E    +R    +     V RARFS
Sbjct: 83  T--KQNYINALKKLAKDADEIIIATDYDREGELIGKEAYHILREVCQVP----VKRARFS 136

Query: 150 AITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLIS 209
           ++T K+I+ A  N  + +   A + +ARQ +DL  G A TR+ +     + G  D   +S
Sbjct: 137 SLTKKEIRKAFENPDEIDFNLADAGEARQIIDLYWGAALTRFLS-LSVRQLGRWD--FLS 193

Query: 210 YGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSRGH----IFDKSTC 265
            G  QTPTL F V+R  +IR F PE YW ++  L+            GH     +D+   
Sbjct: 194 VGRVQTPTLAFIVDREREIRAFDPEDYWKIEALLDKEAQYFYRDLIGGHEAEKFWDEEEA 253

Query: 266 NVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYT 325
              ++ ++  K  TV  V+   ++ + P   NT E +R AS   G+ P  AM+IAE+LYT
Sbjct: 254 EEIYEKLKGAKEATVSSVKKRERTISPPAPFNTTEFLREASKIFGISPKRAMEIAEKLYT 313

Query: 326 QGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKG-KDVGDHPP 384
            GY+SYPRT+ T YP++ D   +L++     ++G +   +L     KP +G K+  DHPP
Sbjct: 314 AGYISYPRTDNTVYPDDLDPKELLKKLSKKKEYGPYAESILEQENIKPTEGKKETTDHPP 373

Query: 385 ITPTKLATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLH 444
           I P  +  R +L  D W++Y+ IVR F+ TL     +     +  V  E+F      L+ 
Sbjct: 374 IHPVDVPKREELSDDEWKVYELIVRRFLATLADPAEWEYLKVELDVNGEIFKASGSRLVE 433

Query: 445 PGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGT 504
            G+  V  +     + +PD + G+ + +  +++  ++T PP   T+S LI  MEK G+GT
Sbjct: 434 EGWHEVYPYEKFDEKELPDLEEGEKLKVNKIEIEAKETQPPKRYTQSSLIKEMEKRGLGT 493

Query: 505 DASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRS 556
            A+    I  + +R Y  V  G    PT LGI ++   +K   E+V   M +
Sbjct: 494 KATRHDIIEKLYKRGY--VIEGDPPRPTDLGIAVIEALEKYAPEIVSEEMTA 543

Length = 822

>gnl|CDD|238110 cd00186, TOP1Ac, DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases

 Score =  362 bits (932), Expect = e-121
 Identities = 116/391 (29%), Positives = 167/391 (42%), Gaps = 49/391 (12%)

Query: 171 ARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRT 230
             +  AR+ LD  +G   +R  TK  + K        +S G  Q+PTLG  VER  +I+ 
Sbjct: 4   VNAQLARRILDRLVGFNLSRLLTKKLRRKGV------LSAGRVQSPTLGLIVEREREIKA 57

Query: 231 FKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSK 290
           F PE YW +                                    K   VV V+   K K
Sbjct: 58  FVPEDYWEI------------------------------------KEAVVVSVEKKEKKK 81

Query: 291 TKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENFDLVAVLR 350
             P    T  L + ASS LG      MQIA++LY  G ++YPRT++T+  E   L A   
Sbjct: 82  NPPPPFTTSTLQQEASSKLGFSAKKTMQIAQKLYEAGLITYPRTDSTRLSEEAILEAREY 141

Query: 351 QQESSPDWGDHVREVLSNGISKPRKGKDVGDHPPITPTKLA----TRTQLDGDAWRLYDY 406
            Q        +   +L    +  R  K+ G H  I PTK+A        L  D ++LY+ 
Sbjct: 142 IQAIYGKEYLYPAPLLGR-RNPKRGKKEQGAHEAIRPTKVAPTPELEANLSEDEFKLYEL 200

Query: 407 IVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNESI-PDFK 465
           I R F+ +   D  Y +      +  E F    K LL  G+  V        E   P  K
Sbjct: 201 IWRRFLASQMADAKYEETTVTLEIGGEKFKASGKVLLEDGWLEVYPEEKDDEEEEPPPLK 260

Query: 466 PGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTS 525
            GD + ++ V++ E++T PP   TE+ LI LMEK GIG  ++    I  +  R YV    
Sbjct: 261 EGDELKLEEVELEEKETQPPPRYTEASLIKLMEKRGIGRPSTYASIIETLLDRGYVEKE- 319

Query: 526 GRRLVPTSLGIVLVHGYQKIDRELVEPTMRS 556
            ++L+PT LG  ++   +K   ELV+P   +
Sbjct: 320 KKKLIPTELGFAVIELLEKHFPELVDPEFTA 350

Topoisomerases clevage single or double stranded DNA and then rejoin the broken phosphodiester backbone. Proposed catalytic mechanism of single stranded DNA cleavage is by phosphoryl transfer through a tyrosine nucleophile using acid/base catalysis. Tyr is activated by a nearby group (not yet identified) acting as a general base for nucleophilic attack on the 5' phosphate of the scissile bond. Arg and Lys stabilize the pentavalent transition state. Glu then acts as a proton donor for the leaving 3'-oxygen, upon cleavage of the scissile strand. Length = 381

>gnl|CDD|216317 pfam01131, Topoisom_bac, DNA topoisomerase

 Score =  321 bits (824), Expect = e-105
 Identities = 120/396 (30%), Positives = 173/396 (43%), Gaps = 56/396 (14%)

Query: 165 KPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVER 224
           + +     + +AR+ LD  IG   +R  T  F  K       ++S G  QTPTLG  VER
Sbjct: 1   EEDENLVDAQEARRILDRLIGFNLSRALTLKFNNK-------VLSAGRVQTPTLGLIVER 53

Query: 225 HDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQ 284
             +I  F PEPYW                                         TV  V+
Sbjct: 54  EKEIENFVPEPYW-----------------------------------------TVKSVE 72

Query: 285 SSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENFD 344
              K +  P   NT  L + AS  LG      M IA++LY  G ++YPRT++T   E+ +
Sbjct: 73  KKEKKEPPPLPFNTSTLQKEASRKLGFSAKKTMDIAQKLYEGGLITYPRTDSTYLSEDAE 132

Query: 345 LVAVLRQQES--SPDWGDHVREVLSNGISKPRKGKDVGDHPPITPTKLATRTQ-LDGDAW 401
           L A+L         D+  +   ++     K      VG H  I PT    R   L  D  
Sbjct: 133 LAAILEYLAKRFGEDYLPYAPLLVK---GKSWGNAKVGAHEAIRPTGPIPRLPELSDDER 189

Query: 402 RLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNE-S 460
           +LYD IVR F+ +     VY +   +  V  E F    K LL PG+  V      ++E  
Sbjct: 190 KLYDLIVRRFLASQMPPAVYEETKVELEVGGEEFKASGKVLLEPGWKKVYPDEKDEDEEP 249

Query: 461 IPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNY 520
           +P+ K G+ + ++ V++ E+KT PP   TE+ LI  MEK GIGT A+    I  + +R Y
Sbjct: 250 LPELKEGEELDVKDVELEEKKTKPPPRYTEASLIKAMEKRGIGTPATRASIIETLLERGY 309

Query: 521 VTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRS 556
           V     ++LVPT LG  L+    +   +LV P + +
Sbjct: 310 VERKKKKKLVPTDLGRALIDALPRFP-DLVSPELTA 344

This subfamily of topoisomerase is divided on the basis that these enzymes preferentially relax negatively supercoiled DNA, from a 5' phospho- tyrosine linkage in the enzyme-DNA covalent intermediate and has high affinity for single stranded DNA. Length = 365

>gnl|CDD|180892 PRK07220, PRK07220, DNA topoisomerase I; Validated

 Score =  305 bits (783), Expect = 6e-95
 Identities = 161/505 (31%), Positives = 254/505 (50%), Gaps = 27/505 (5%)

Query: 58  GHIMGLDFTSKYNNWDKVDPLELF-----SCPTEKREATPKLKLPAFLANEAKDCEFLVL 112
           GHI+ +DF  +YNNW KVD  +L      + PT+K+  T   KL        K+ + + +
Sbjct: 51  GHIVNIDFPKEYNNWQKVDARDLIDAEIITTPTQKKIVTALKKL-------GKEADRVTI 103

Query: 113 WLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNLVKPNIFEAR 172
             D D+EGE I  E +  ++    +N      R R+SAIT K+I+ A  N V+ +   A 
Sbjct: 104 ATDYDREGELIGVEALNIIK---KVNPDIKFDRVRYSAITKKEIERAFSNPVEVDFNLAD 160

Query: 173 SVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFK 232
           +  +RQ +DL  G A TRY      G+ G      +S G  Q+PTL   V+R  +   F 
Sbjct: 161 AGHSRQVIDLVWGAALTRY-ISLAAGRLGK---MFLSVGRVQSPTLALIVDREKEREAFV 216

Query: 233 PEPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTK 292
           P PYW +  TL  NG       S    ++K   +  F+ + K     V +V+  TK+   
Sbjct: 217 PTPYWEIYATLENNGETFVAQHSTRRFWEKEEADRVFEKLGKT--AEVTEVEKGTKTDKP 274

Query: 293 PQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENFDLVAVLRQQ 352
           P   NT E +  A+S +G    +AM+IAE LYT GY+SYPRT+ T YPE+ DL   +   
Sbjct: 275 PTPFNTTEFISAANS-IGFSAANAMRIAESLYTNGYISYPRTDNTVYPESLDLREQIEIF 333

Query: 353 ESSPDWGDHVREVLSNGISKPRKGK-DVGDHPPITPTKLATRTQLDGDAWRLYDYIVRHF 411
              P +G++ +++L  G   P +GK +  DHPPI P  LA +++L  D W++Y+ +VR F
Sbjct: 334 AEGP-FGEYAQKLLEKGELVPTRGKKETTDHPPIYPASLAKKSELKEDEWKVYELVVRRF 392

Query: 412 IGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNESIPDFKPGDLIP 471
             T  G   +     +F +  E F      L  PG+     ++A ++  +P+   G+ + 
Sbjct: 393 FATFAGPAEWETMKLRFDIGGEEFRANGSRLTEPGWRWYYPYNAPEDRLLPELSEGEELK 452

Query: 472 IQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGRRLVP 531
           ++  +M++++T PP    +  LI LME  G+GT A+    I+ +  R Y+    G  + P
Sbjct: 453 VKKKEMLDKETQPPGRYGQGRLIKLMEDLGLGTKATRHEIISKLYSRAYI---HGNPIQP 509

Query: 532 TSLGIVLVHGYQKIDRELVEPTMRS 556
           T+    +V   +K    + +P M S
Sbjct: 510 TNTAFAVVDALEKYAPTITKPDMTS 534

Length = 740

>gnl|CDD|214663 smart00437, TOP1Ac, Bacterial DNA topoisomerase I DNA-binding domain

 Score =  256 bits (656), Expect = 6e-82
 Identities = 86/258 (33%), Positives = 126/258 (48%), Gaps = 10/258 (3%)

Query: 288 KSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENFDLVA 347
           K K  P    T  L + AS  LG      MQIA++LY +G ++YPRT++T+  E   L A
Sbjct: 5   KKKNPPPPFTTSTLQQEASRKLGFSAKKTMQIAQKLYEKGLITYPRTDSTRLSEEAVLEA 64

Query: 348 VLR-QQESSPDWGDHVREVLSNGISKPRKGKD-VGDHPPITPTKLATRTQ----LDGDAW 401
               Q+    ++ D    +L     KPRKGK   G H  I PTK     +    L  D +
Sbjct: 65  RNYIQKLYGKEYLDLAVVLLKPR--KPRKGKKAQGAHEAIRPTKPIFTPELEKELSEDEF 122

Query: 402 RLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTW-SAMKNES 460
           +LY+ I R F+ +   D  Y +      +  E F  + K LL  G+  V       +   
Sbjct: 123 KLYELIWRRFLASQMPDAKYEETKVTIKIGGEKFKAKGKTLLFDGWLKVYPEEKKEEEIE 182

Query: 461 IPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNY 520
           +P  K GD + ++ V++ E++T PP   TE+ LI LMEK GIG  ++    I  +  R Y
Sbjct: 183 LPTLKKGDELKVEEVEVEEKETKPPARYTEASLIKLMEKRGIGRPSTYASIIETLLDRGY 242

Query: 521 VTVTSGRRLVPTSLGIVL 538
           VT    ++L+PT LGI +
Sbjct: 243 VTKK-KKKLIPTELGIAV 259

Bacterial DNA topoisomerase I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase alpha subunit. Length = 259

>gnl|CDD|184936 PRK14973, PRK14973, DNA topoisomerase I; Provisional

 Score =  265 bits (680), Expect = 1e-78
 Identities = 169/518 (32%), Positives = 247/518 (47%), Gaps = 32/518 (6%)

Query: 45  FGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVD--PLELFSC-----PTEKREATPKLKLP 97
           F D V+  +    GH++ +DF   Y NW   +  P  L        PTEK+      KL 
Sbjct: 38  FDDTVVVGLR---GHVVEVDFEPGYTNWRSEEHTPRSLIDADTIKKPTEKKIVGLIQKL- 93

Query: 98  AFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIK 157
                 AK  + + +  D D EGE I  E  E VR  +N   P  + RARFSAIT ++I 
Sbjct: 94  ------AKKADRVTIATDFDTEGELIGKEAYELVR-AVNPKVP--IDRARFSAITKEEIV 144

Query: 158 AAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPT 217
            A       +   A + +ARQ +DL  G + TR+ +       G    +++S G  Q+PT
Sbjct: 145 TAFAEPTDLDFALAAAGEARQIIDLIWGASLTRFIS--LAAHRGG--DNILSVGRVQSPT 200

Query: 218 LGFCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKH 277
           L   V+R  +I  F PE YW+L L    +G  +    + G   D +     + A ++   
Sbjct: 201 LAMIVDREKEIEAFVPEKYWMLSLATEKDGEGIEARHTHGRFTDSAAAEAAYDATKEPLV 260

Query: 278 VTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETT 337
           VT  +V+   K    P   +T   + VA+S LG    +AM+IAE LY  GY+SYPRT+ T
Sbjct: 261 VT--EVKEGHKVDRAPTPFDTTTFI-VAASRLGFSAANAMRIAEDLYMNGYISYPRTDNT 317

Query: 338 QYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGK-DVGDHPPITPTKLATRTQL 396
            YP++ DL  VL        +   V  V  N    P +GK    DHPPI PT +ATR +L
Sbjct: 318 IYPKSLDLNGVLATLAKGA-FSKDVAWVKDNRRPVPTRGKKSSTDHPPIHPTGVATREEL 376

Query: 397 DGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAM 456
             D W+LY+ +VR F+ TL  D  +      F    E +T     LL  G+  V  +S  
Sbjct: 377 GDDRWKLYELVVRRFLATLSPDAEWATMKVNFDAGGEPYTATGGRLLEAGWRTVYPYSEA 436

Query: 457 KNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNIC 516
           K   +P F  G+ +PI +V + E++T PP   ++S LI  ME+ G+GT ++    I  + 
Sbjct: 437 KENILPAFALGEKLPILAVNLEEKETQPPARYSQSRLIQRMEELGLGTKSTRHEVIGKLV 496

Query: 517 QRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTM 554
            R Y+    G  L PT +G  +    ++    + EP M
Sbjct: 497 SRKYI---EGNPLRPTLVGRAVTESLEEHAGTITEPDM 531

Length = 936

>gnl|CDD|235602 PRK05776, PRK05776, DNA topoisomerase I; Provisional

 Score =  206 bits (526), Expect = 1e-58
 Identities = 121/449 (26%), Positives = 197/449 (43%), Gaps = 23/449 (5%)

Query: 115 DCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNLVKPNIFEARSV 174
           D D EG  I + +++       +  PK   R +FSA+T  DI+ A  NL   +     + 
Sbjct: 105 DYDIEGSVIGYLIIK------YLGDPKKAKRMKFSALTKSDIRRAFRNLETLDYEMINAG 158

Query: 175 DARQELDLRIGCAFTRYQTKFFQGKYGDLDAS----LISYGPCQTPTLGFCVERHDKIRT 230
            AR ELD   G   +R      +      DAS    ++S G  Q+PTL + VER  +   
Sbjct: 159 IARHELDWLWGINVSRALMSSVR------DASGKRVILSAGRVQSPTLKYVVEREIERNL 212

Query: 231 FKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSK 290
           F P PY+ + + +  NG   ++ +       K       + ++K  ++ V  V+   +  
Sbjct: 213 FVPLPYFSVSIIIEKNGYEFTLKYENKKFETKEEAKEILEEIKKTGYLKVTKVEVKIEIL 272

Query: 291 TKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENFDLVAVLR 350
             P   N  +L   A+   G  P+    IAE LY  G +SYPRT + + P   ++  +L+
Sbjct: 273 EPPPPFNLGDLQVEAARIYGFSPYKTQSIAEDLYLDGLISYPRTNSQKLPPTLNIRNILK 332

Query: 351 QQESSPDWGDHVREVLS--NGISKPRKG-KDVGDHPPITPTKLATRTQLDGDAWRLYDYI 407
               SP +   V  +L    G+ KP +G KD   HP I PT       L  D ++LYD I
Sbjct: 333 GLSRSPQYRPLVNLLLKETKGVLKPVQGPKDDPAHPAIYPTGEPP-KNLSKDEFKLYDLI 391

Query: 408 VRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYL--LHPGFTGVMTWSAMKNESIPDFK 465
           VR F+ +     V +  +    V        A        G+     +     E +P  K
Sbjct: 392 VRRFLASFAAPAVLSNTIVTLRVPGFPLVFSASGQRIEERGWLKYYPFHKFDEEELPLLK 451

Query: 466 PGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTS 525
            G+ + I  VK+ +  T PP   +++ L+  ME  GIGT+A+    I  + +R Y+T ++
Sbjct: 452 KGERVKIVDVKVRKSYTKPPSRYSKASLLKWMESVGIGTEATRARIIETLFKRGYLT-SN 510

Query: 526 GRRLVPTSLGIVLVHGYQKIDRELVEPTM 554
           G+ +  T LG  +    +K   ++V   +
Sbjct: 511 GKYIEVTPLGFGVAEVLEKYFPDIVSVEL 539

Length = 670

>gnl|CDD|233253 TIGR01057, topA_arch, DNA topoisomerase I, archaeal

 Score =  203 bits (518), Expect = 7e-58
 Identities = 115/452 (25%), Positives = 194/452 (42%), Gaps = 11/452 (2%)

Query: 104 AKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNL 163
           AK  +  +   D D EGE I F+ ++       +   K   R +FS +T +DI+ A  N 
Sbjct: 91  AKGADEYINACDYDIEGEVIGFKALKYF---CGVERAK---RMKFSTLTKQDIRRAYANP 144

Query: 164 VKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVE 223
            + +     +  AR  LD   G   +R   +  +   G     ++S G  Q PTL F VE
Sbjct: 145 EEIDYGMVDAGMARHILDWYWGINLSRALMEAIRAAAGRW--VILSAGRVQGPTLAFLVE 202

Query: 224 RHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDV 283
           R  +I  F P+PYW++  TL   G        +  I+ +       + ++K     V +V
Sbjct: 203 REREINLFVPKPYWVIKATLEKGGGVFDARPEKWKIWSEEEAKSIKEELKKSPWAAVEEV 262

Query: 284 QSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENF 343
           +S       P   +   L R A    G  P     IA+ LY +  +SYPRT + + P + 
Sbjct: 263 RSERSILKPPPPFDLGTLQREAYRIFGFSPKKTQSIAQELYEEALISYPRTSSQKLPPSI 322

Query: 344 DLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVGD-HPPITPTKLATRTQLDGDAWR 402
           +  A+L      P + +    +L  G+ KP +GK     HP I PT      +L  D  +
Sbjct: 323 NYRAILDNLAKGPLYREAAERLLETGVLKPVEGKKEDPAHPAIHPTGEIPSQELSKDEKK 382

Query: 403 LYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNESIP 462
           +YD IVR F+     + +  +      +  E F +    ++  G+     +S  + + +P
Sbjct: 383 VYDLIVRRFLAAFSEEAIREKSKVLLRIGQEKFRLSGLRVVKLGWLEYYHYSKFEEKELP 442

Query: 463 DFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVT 522
               GD I +  V +  ++T PP    ++ LI  ME  G+GT A+    I  + +R Y  
Sbjct: 443 PLDRGDKIKVVRVDVRVKETQPPARYDKASLIREMESRGLGTKATRARIIETLYKRGY-- 500

Query: 523 VTSGRRLVPTSLGIVLVHGYQKIDRELVEPTM 554
           +   + +  T LG  ++   Q+   E++   +
Sbjct: 501 IEGKKSIKVTPLGEAVIETLQRYCPEIISEEL 532

This model describes topoisomerase I from archaea. These enzymes are involved in the control of DNA topology. DNA topoisomerase I belongs to the type I topoisomerases, which are ATP-independent [DNA metabolism, DNA replication, recombination, and repair]. Length = 618

>gnl|CDD|236078 PRK07726, PRK07726, DNA topoisomerase III; Provisional

 Score =  169 bits (432), Expect = 2e-45
 Identities = 121/473 (25%), Positives = 191/473 (40%), Gaps = 71/473 (15%)

Query: 115 DCDKEGENICFEVME--AVRHQININSPKTVWRARFSAITDKDIKAAMWNLVKPNI-FE- 170
           D D+EGE I  E+++   VR  I     K +W    S++TDK IK A  NL KP      
Sbjct: 101 DADREGELIAREILDYCGVRKPI-----KRLW---ISSLTDKAIKRAFANL-KPGKETIP 151

Query: 171 -ARSVDARQELDLRIGCAFTR-YQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKI 228
              S  AR   D  +G   TR Y     +  Y  +    +S G  QTPTL   V R ++I
Sbjct: 152 LYYSALARSRADWLVGINMTRAYTLLGRKAGYNGV----LSVGRVQTPTLALVVRRDEEI 207

Query: 229 RTFKPEPYWLLDLTLNLNGVAVSVTW--------SRGHIFDKSTCNVFFKAVEK--EKHV 278
             F P+PYW ++  L   G   +  W          G + D+       + V +   +  
Sbjct: 208 ENFVPKPYWEVEAHL-TPGERFTAKWQPSEPYQDEEGRLLDRPLAE---QVVARIQGQPA 263

Query: 279 TVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLY-TQGYVSYPRTETT 337
            V +V++  K +  P   +  EL   A+   G+     + IA+ LY T   ++YPRT++ 
Sbjct: 264 KVTEVETKRKKEYAPLLYDLSELQIDANKRFGLSAKETLDIAQSLYETHKLITYPRTDSR 323

Query: 338 QYPEN-FDLV-AVLRQQESSPDWGDHVREVLSNGISKPRKG----KDVGDHPPITPT-KL 390
             PE+    +  VL        +      VL   I   R      K V  H  I PT + 
Sbjct: 324 YLPEDMVATLPEVLNAISKVDPYLLLAPPVLDPSI---RSRAWNDKKVTAHHAIIPTEQP 380

Query: 391 ATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGV 450
              ++L  D  ++YD I R ++        Y +   +  +A   F  + K ++  G+  +
Sbjct: 381 PNLSKLSEDERKVYDLIARRYLAQFLPPAEYDKTTIELEIAGGTFIAKGKQVVEAGWKAL 440

Query: 451 MTWSAMKNE---SIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLM---------- 497
           +       E    +P    GD + ++  ++ E +T PP   TE  L+S M          
Sbjct: 441 LGKKEEDEEKEQPLPVLAKGDELKVEKGEVKEGQTQPPKRFTEGTLLSAMENIARFVQDK 500

Query: 498 -------EKHGIGTDA---SIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVH 540
                  E  G+GT+A    I   I  + +R Y+    G+ +  T  G  L+ 
Sbjct: 501 ELKKTLKETDGLGTEATRAGI---IEKLFKRGYLEKK-GKYIHATDKGKQLID 549

Length = 658

>gnl|CDD|233252 TIGR01056, topB, DNA topoisomerase III, bacteria and conjugative plasmid

 Score =  156 bits (397), Expect = 6e-41
 Identities = 119/529 (22%), Positives = 222/529 (41%), Gaps = 64/529 (12%)

Query: 58  GHIMGL----DFTSKYNNWDKVDPLELFSCPTEKREATPKLKLPAFLAN-----EAKDCE 108
           GH++ L    ++  KY NW +   L L     E  +     K            +    +
Sbjct: 42  GHLVELAEPEEYDEKYKNW-RTYDLPLEP---EDWQLVVSDKTKKQFNVIKRILKENKVD 97

Query: 109 FLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNLVKPNI 168
            +V+  D D+EGE I  E+++     + +    T+ R   S++ D  I+ A  NL   + 
Sbjct: 98  EVVIATDPDREGELIAREILD----YLKVTDKVTIKRLWISSLVDSSIRKAFKNLRPKSE 153

Query: 169 FEA--RSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHD 226
            E   +S  AR   D  +G   TR  TK   G+    D  ++S G  QTPTL   V+R +
Sbjct: 154 TEGLYKSGVARARADWLVGINLTRAFTKL--GREAGNDG-VLSVGRVQTPTLAMVVKREN 210

Query: 227 KIRTFKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTC---NVFFKAVE--KEKHVTVV 281
           +I+ F  +P++ +  T+N +    +  W + +  ++       +    V    +K   V 
Sbjct: 211 EIKNFVGKPFYEVSATINKDEQEFTTEW-QPYKDEEERELHEFLAENVVTDLTQKPALVT 269

Query: 282 DVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLY-TQGYVSYPRTETTQYP 340
           D++   K  + P   +   L   A+   G+     + IA++LY T   ++YPRT++   P
Sbjct: 270 DIEKERKKTSAPLFYDLSALQEDANKRFGISAKRTLDIAQKLYETHKLITYPRTDSRYLP 329

Query: 341 ENFDLVAVLRQ-----QESSPDW--GDHVREVLSNGISKPRKGKDVGDHPPITPTK-LAT 392
           E  D   +L +     +  +P         E+ +N +   +K   + DH  I PT     
Sbjct: 330 E--DEKEMLLEVLDALKVITPALLPIKKRDELTNNRLWNDKK---IEDHHAIIPTGNDFN 384

Query: 393 RTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMT 452
            + L  +   +Y  I ++++        Y     + ++   MF  + K L   G+  ++ 
Sbjct: 385 LSDLSEEERNVYKLIAQNYLMQFMPKEEYETTTIEIAIGKLMFEAKGKILQDNGWKALLG 444

Query: 453 WSAMKNE----SIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLM----------- 497
                 E    ++P F+ GD + +++++++E++T PP   TE  L+S M           
Sbjct: 445 KQEEDEETEDTTLPAFQKGDELDVETLELLEKQTKPPARYTEGTLLSAMTNPAAFVQDKG 504

Query: 498 ------EKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVH 540
                 E  G+GT+A+    I N+ +R ++      ++  T  G +L  
Sbjct: 505 LKKTLKETKGLGTEATRADIIENLFKRGFIQK-KKNKIYITKNGKLLCL 552

This model describes topoisomerase III from bacteria and its equivalents encoded on plasmids. The gene is designated topB if found in the bacterial chromosome, traE on conjugative plasmid RP4, etc. These enzymes are involved in the control of DNA topology. DNA topoisomerase III belongs to the type I topoisomerases, which are ATP-independent [DNA metabolism, DNA replication, recombination, and repair]. Length = 660

>gnl|CDD|233249 TIGR01051, topA_bact, DNA topoisomerase I, bacterial

 Score =  151 bits (383), Expect = 3e-39
 Identities = 135/538 (25%), Positives = 222/538 (41%), Gaps = 72/538 (13%)

Query: 51  FKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPTEKREATPKLKLPAFLANEAKDCEFL 110
           +++ +  GHI  L  +    + +K D    +     K++   +LK        AK  + +
Sbjct: 21  YEVEASMGHIRDLPKSRLGVDIEK-DFEPEYVVSKGKKKVVKELK------TLAKKADEV 73

Query: 111 VLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNLVKPNIFE 170
            L  D D+EGE I + + E ++ +  +       R  F+ IT K I+AA+ N  + ++  
Sbjct: 74  YLATDPDREGEAIAWHLAEVLKPKDPVYK-----RIVFNEITKKAIRAALKNPREIDMNL 128

Query: 171 ARSVDARQELDLRIGCAFTR-YQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIR 229
             +  AR+ LD  +G   +     K  +G          S G  Q+  L   V+R  +I+
Sbjct: 129 VNAQQARRILDRLVGYTLSPLLWKKVAKGL---------SAGRVQSVALRLIVDREREIK 179

Query: 230 TFKPEPYWLLDLTLNLNGVAVSVTWSR--------GHIFDKSTCNVFFKAVEKEKHVTVV 281
            F PE YW +D T            +         G   D++      + ++ E+ V   
Sbjct: 180 RFVPEEYWTIDATFQKGEETFEALLTEVNGKKLKAGSDLDEAEATALKEQLKGEELVVEE 239

Query: 282 DVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLY--------TQGYVSYPR 333
             +   KS+  P    T  L + AS  LG      M IA+RLY        T G ++Y R
Sbjct: 240 IEKKPKKSRPPP-PFTTSTLQQEASRKLGFSAKKTMMIAQRLYEGVSTGDGTIGLITYMR 298

Query: 334 TETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPR----KGKDVGD-HPPITPT 388
           T++T+       V   R      ++G    E L     KP+    K K+  + H  I PT
Sbjct: 299 TDSTRLSNQA--VNEARNLIDK-NYGK---EYLG---PKPKRYKSKEKNAQEAHEAIRPT 349

Query: 389 KL-----ATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEA--KY 441
            +       +  L  D +RLY+ I + F+ +   D  Y     + +  D  +  +A  + 
Sbjct: 350 SVFRTPEELKDYLKRDEFRLYELIWKRFVASQMADARYDSTSVRLTNEDGEYVFKATGRK 409

Query: 442 LLHPGFTGVM-----TWSAMKNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISL 496
           L+  G+  V           K+  +P  K GD + +  VK  +  T PP   TE+ L+  
Sbjct: 410 LIFDGYYKVYVEGSDDPLEEKDRILPPLKEGDAVKLVEVKPNQHFTQPPARYTEASLVKE 469

Query: 497 MEKHGIG---TDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVE 551
           +E+ GIG   T ASI   I+ I  R YV     +RL PT LG  +    +K   ++V+
Sbjct: 470 LEELGIGRPSTYASI---ISTIQDRGYVKKE-NKRLYPTELGFAVTDLLEKHFGDVVD 523

This model describes DNA topoisomerase I among the members of bacteria. DNA topoisomerase I transiently cleaves one DNA strand and thus relaxes negatively supercoiled DNA during replication, transcription and recombination events [DNA metabolism, DNA replication, recombination, and repair]. Length = 610

>gnl|CDD|173782 cd03362, TOPRIM_TopoIA_TopoIII, TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III

 Score =  131 bits (333), Expect = 3e-36
 Identities = 43/115 (37%), Positives = 61/115 (53%), Gaps = 6/115 (5%)

Query: 51  FKMTSVCGHIMGLDFTSKYNNWDKVDPLE--LFSCPTEKREATPKLKLPAFLANEAKDCE 108
           + +T   GH++ LDF  +Y+ WDKV PLE  LF  P + +    K K    L   AK  +
Sbjct: 41  YVVTWASGHLLELDFPEEYDPWDKVWPLEDPLFPAPFKLKVDKGKKKQFKVLKKLAKRAD 100

Query: 109 FLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNL 163
            +V+  D D+EGE I  E++E  +        K V RA FS++T K I+ A  NL
Sbjct: 101 EIVIATDADREGELIGREILEYAKCVKR----KPVKRAWFSSLTPKAIRRAFKNL 151

Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. Length = 151

>gnl|CDD|235516 PRK05582, PRK05582, DNA topoisomerase I; Validated

 Score =  136 bits (344), Expect = 8e-34
 Identities = 124/536 (23%), Positives = 200/536 (37%), Gaps = 103/536 (19%)

Query: 51  FKMTSVCGHI-------MGLDFTSKYNNWD---KVDPLELFSCPTEKREATPKLKLPAFL 100
           +K+ +  GHI       +G+D     NN++                K     +LK     
Sbjct: 25  YKVVASMGHIRDLPKSQLGIDIE---NNFEPKYITIR--------GKGPVIKELK----- 68

Query: 101 ANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAM 160
              AK  + + L  D D+EGE I + +   +   ++        R  F+ IT   IK A 
Sbjct: 69  -KAAKKAKKVYLATDPDREGEAIAWHLAHIL--GLDEKEKN---RIVFNEITKDAIKNAF 122

Query: 161 WNLVKPNIFEARSVDA---RQELDLRIGCAFTRY------QTKFFQGKYGDLDASLISYG 211
            N  K ++     VDA   R+ LD  +G     Y        K  +G          S G
Sbjct: 123 KNPRKIDMN---LVDAQQARRILDRLVG-----YKLSPLLWKKVKKGL---------SAG 165

Query: 212 PCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLN-----LNGVAVSVTWSRGHIFDKSTCN 266
             Q+  L   ++R  +IR F PE YW +D                    +  + ++    
Sbjct: 166 RVQSVALKLIIDREKEIRAFVPEEYWTIDAEFKKGKKKFEASFYGYKGKKIELKNEEDVK 225

Query: 267 VFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLY-- 324
                ++K+    V  V+   + +  P    T  L + A+  L       M IA++LY  
Sbjct: 226 EILAELKKKDFK-VSKVKKKERKRNPPPPFTTSTLQQEAARKLNFSTKKTMMIAQQLYEG 284

Query: 325 -------TQGYVSYPRTETTQYPENFDLVAVLRQQESSP----DWGDHVREVLSNGISKP 373
                  T G ++Y RT++T+  +         Q+E+       +G    E L       
Sbjct: 285 IDLGKQGTVGLITYMRTDSTRISDTA-------QEEAREFIEEKYGK---EYLPKKPKVY 334

Query: 374 RKGKDVGD-HPPITPTKLATRT------QLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVA 426
           +K     D H  I PT +   T       L  D  +LY  I   F+ +     V+     
Sbjct: 335 KKKSGAQDAHEAIRPTSV-FLTPESAKKYLTKDQLKLYKLIWNRFVASQMAPAVFDTVSV 393

Query: 427 KFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKMVERKTTPPD 486
                   F      +   GF  V      K++ +P+ + G+ + ++ ++  +  T PP 
Sbjct: 394 DLENNGVKFRASGSKVKFDGFMKVYVGDEEKDKMLPELEEGEKVKLKKIEPEQHFTQPPA 453

Query: 487 YLTESELISLMEKHGIG---TDASIPVHINNICQRNYVTVTSGRRLVPTSLG-IVL 538
             TE+ LI  +E+ GIG   T A     I+ I +R YV +   +RLVPT LG IV 
Sbjct: 454 RYTEASLIKTLEELGIGRPSTYAPT---ISTIQKRGYVKLEK-KRLVPTELGEIVN 505

Length = 650

>gnl|CDD|173778 cd01028, TOPRIM_TopoIA, TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IA family of DNA topoisomerases (TopoIA)

 Score =  123 bits (310), Expect = 4e-33
 Identities = 42/113 (37%), Positives = 59/113 (52%), Gaps = 5/113 (4%)

Query: 51  FKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPTEKREATPKLKLPAFLANEAKDCEFL 110
           + +T+  GH++ L F  +Y +WDK  PLELF    +      K K    L   AK  + +
Sbjct: 35  YVVTASVGHLLELPFPEEYVDWDKDWPLELFPFEPKYVVIPDKKKQLKALKKLAKKADEI 94

Query: 111 VLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNL 163
           VL  D D+EGE I +E++E ++        K V RA FS IT K I+ A  NL
Sbjct: 95  VLATDPDREGELIAWEILEVLK-----CDNKPVKRAWFSEITPKAIREAFKNL 142

This subgroup contains proteins similar to the Type I DNA topoisomerases: E. coli topisomerases I and III, eukaryotic topoisomerase III and, ATP-dependent reverse gyrase found in archaea and thermophilic bacteria. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA. These enzymes cleave one strand of the DNA duplex, covalently link to the 5' phosphoryl end of the DNA break and allow the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. Length = 142

>gnl|CDD|214662 smart00436, TOP1Bc, Bacterial DNA topoisomeraes I ATP-binding domain

 Score =  110 bits (277), Expect = 3e-29
 Identities = 35/93 (37%), Positives = 48/93 (51%), Gaps = 7/93 (7%)

Query: 145 RARFSAITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLD 204
           R  FS IT K I+ A+ N  + +     +  AR+ LD  IG   +R  TK  +       
Sbjct: 3   RIEFSEITKKAIREALKNPREIDENLVNAQLARRILDRLIGFNLSRLLTKKLR------- 55

Query: 205 ASLISYGPCQTPTLGFCVERHDKIRTFKPEPYW 237
             ++S G  QTPTLG  VER  +I+ F P+PYW
Sbjct: 56  NGVLSAGRVQTPTLGLIVEREREIKNFVPKPYW 88

Extension of TOPRIM in Bacterial DNA topoisomeraes I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase beta subunit. Length = 89

>gnl|CDD|233251 TIGR01054, rgy, reverse gyrase

 Score =  120 bits (302), Expect = 2e-28
 Identities = 99/452 (21%), Positives = 180/452 (39%), Gaps = 66/452 (14%)

Query: 104  AKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNL 163
            A + + + +  D D EGE I +++   +    N N    V RA F  +T + I  A+ + 
Sbjct: 717  AHEVDEVFIGTDPDTEGEKIGWDLALLLS-PYNPN----VKRAEFHEVTRRAILEALESP 771

Query: 164  --VKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFC 221
              V  N+ +A+ V  R+  D  IG   ++   + F  ++       +S G  QTP LG+ 
Sbjct: 772  RSVDENLVKAQVV--RRIEDRWIGFTLSQKLWEAFNKRW-------LSAGRVQTPVLGWI 822

Query: 222  VERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVV 281
            ++R+ + R  +      L +    +   + +        ++     F K       + V 
Sbjct: 823  IDRYRESREKRGY----LLIFALESDFRLGLEHD-----NRLEAKEFEK---DLTWLDVE 870

Query: 282  DVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPE 341
            D+    + +       T  ++  A+  LG+     MQIA+ L+  G ++Y RT++T+  +
Sbjct: 871  DIAEREEERNPLPPYTTDTMLEDANRKLGLSVKETMQIAQELFENGLITYHRTDSTRVSD 930

Query: 342  NFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVGDHPPITPTK-----------L 390
                VA            +++   L      PR+  + G H  I PT+           L
Sbjct: 931  VGMRVAK-----------EYLASRLGGEYFYPREWGEGGAHECIRPTRPLDVDDLQRLIL 979

Query: 391  ATRTQLDGDAW---RLYDYIVRHFIGTLC--GDLVYTQKVAKFSVADEMFTMEAKYLLHP 445
                +L+G      RLYD I R F+ +      +   +   K    +       + +   
Sbjct: 980  EGVIELEGLTREHLRLYDLIFRRFMASQMRPAKVDTKEITLKADGKEAEEEGIVEIVER- 1038

Query: 446  GFTGVMTWSAMKNESIPDFKPGDLIPIQSVKMVERKTTPPDYL-TESELISLMEKHGIGT 504
            GF  V  +   +   +             VK  E ++ P  Y  T+ E++  M++ GIG 
Sbjct: 1039 GFELV--YPLWRKNELEKGSTFI------VKDKELRSVPKVYPYTQGEIVQEMKERGIGR 1090

Query: 505  DASIPVHINNICQRNYVTVTSGRRLVPTSLGI 536
             ++    +  + +R YV V S   L+PT LGI
Sbjct: 1091 PSTYATIVEKLLRRGYV-VESKGFLIPTKLGI 1121

This model describes reverse gyrase, found in both archaeal and bacterial thermophiles. This enzyme, a fusion of a type I topoisomerase domain and a helicase domain, introduces positive supercoiling to increase the melting temperature of DNA double strands. Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA [DNA metabolism, DNA replication, recombination, and repair]. Length = 1171

>gnl|CDD|236172 PRK08173, PRK08173, DNA topoisomerase III; Validated

 Score =  119 bits (299), Expect = 4e-28
 Identities = 135/541 (24%), Positives = 213/541 (39%), Gaps = 90/541 (16%)

Query: 53  MTSVCGHIMGL----DFTSKYNNWD----KVDPLELFSCPTEKREATPKLKLPAFLANEA 104
           ++S  GH++ +    ++  K   W      V P      P  K E+  +LK+   L    
Sbjct: 38  LSSAVGHLLEIAAPEEYEVKRGKWSFAHLPVIPPHFDLNPIAKTES--RLKVLTKLIKR- 94

Query: 105 KDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNL- 163
           KD   L+   D  +EGE I F ++   +H     + K V R    ++T + I+    NL 
Sbjct: 95  KDVTRLINACDAGREGELI-FRLI--AQH---AKAKKPVKRLWLQSMTPQAIRDGFANLR 148

Query: 164 ----VKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLG 219
               ++P    AR    R E D  +G   TR  T F   K G     L + G  QTPTL 
Sbjct: 149 SDEDMQPLADAARC---RSEADWLVGINGTRAMTAF-NSKGGGF--FLTTVGRVQTPTLS 202

Query: 220 FCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVT 279
             VER +KIR F P  YW +              W     FD       FK  E +    
Sbjct: 203 IVVEREEKIRRFVPRDYWEVRAEFVAAAGFYEGRW-----FDPK-----FKKDEFDPEKR 252

Query: 280 ----------------------VVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAM 317
                                  V  +S   ++  P   +   L R A+   G    + +
Sbjct: 253 ASRLWSEAAAEAIVAACRGKPGTVTEESKPSTQLSPLLFDLTSLQREANGRFGFSAKNTL 312

Query: 318 QIAERLYTQGYV-SYPRTETTQYPENFDLVAVLRQ----QESSPDWGDHVREVLSNGISK 372
            +A+ LY +  V +YPRT++   PE  D +  ++Q     + S ++  H +++L  G  K
Sbjct: 313 GLAQALYEKHKVLTYPRTDSRALPE--DYLGTVKQTLEMLKESNNYLPHAKQILDKGWVK 370

Query: 373 PRK----GKDVGDHPPITPTKLATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKF 428
           P K       + DH  I PT  A ++  + +  +LYD +V+ F+        +       
Sbjct: 371 PNKRIFDNSKISDHFAIIPTLQAPKSLSEPEQ-KLYDLVVKRFLAVFFPAAEFLVTTRIT 429

Query: 429 SVADEMFTMEAKYLLHPGFTGVMTWSAM-KNESIPDFKPGDLIPIQSVKMVERKTTPPDY 487
            VA   F  E K L++PG+  V    A   + ++   + G+ +    ++ V   T PP  
Sbjct: 430 EVAGHHFKTEGKVLVNPGWLAVYGKEAQGADANLVPVQKGEKVKTDKIEAVALTTKPPAR 489

Query: 488 LTESELISLME----------------KHGIGTDASIPVHINNICQRNYVTVTSGRRLVP 531
             E+ L+S ME                + G+GT A+    I  +    Y+ V  GR L+P
Sbjct: 490 YNEATLLSAMEGAGKLVEDDELREAMAEKGLGTPATRAAIIEGLLGEKYL-VREGRELIP 548

Query: 532 T 532
           T
Sbjct: 549 T 549

Length = 862

>gnl|CDD|224035 COG1110, COG1110, Reverse gyrase [DNA replication, recombination, and repair]

 Score =  117 bits (295), Expect = 2e-27
 Identities = 119/484 (24%), Positives = 193/484 (39%), Gaps = 86/484 (17%)

Query: 82   SCPTEKRE----ATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQINI 137
             CP          T  ++    LA E    + +++  D D EGE I ++V   +R     
Sbjct: 710  KCPRCGSRNVEDKTETVEALRELALEV---DEILIGTDPDTEGEKIAWDVFNYLR----- 761

Query: 138  NSPKT--VWRARFSAITDKDIKAAMWNL--VKPNIFEARSVDARQELDLRIGCAFTRYQT 193
              P    V R  F  +T + I  A+ N   V  N+ +A+ V  R+  D  IG   ++   
Sbjct: 762  --PYNPNVKRIEFHEVTRRAILEALKNPRDVDENLVKAQIV--RRIEDRWIGFELSQKLW 817

Query: 194  KFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVT 253
              F  K        +S G  QTP LG+ V R+++ +  +      LDL L          
Sbjct: 818  DVFNNKN-------LSAGRVQTPVLGWIVNRYEEYKEKRGYLVIQLDLDLPSG------- 863

Query: 254  WSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGP 313
             +R  + +        K   K   V VVDV    + K       T  ++R AS  L +  
Sbjct: 864  -NREEVEN-------VKRKLKLIVVEVVDVVEREEEKNPLPPYTTDTMLRDASRRLRLSA 915

Query: 314  HHAMQIAERLYTQGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKP 373
               MQIA+ L+  G ++Y RT++T+  +    VA            +++R+       +P
Sbjct: 916  DETMQIAQDLFEGGLITYHRTDSTRVSDVGIRVAR-----------EYLRKEFGEEYFRP 964

Query: 374  RKGKDVGDHPPITPTK---------------LATRTQLDGDAWRLYDYIVRHFIGTLCGD 418
            R   + G H  I PT+               +    +L  +  R+YD I R F+ +    
Sbjct: 965  RSWGEEGAHEAIRPTRPIDVEELITLIEEGVIQLPIRLTKNHLRVYDLIFRRFMASQMRP 1024

Query: 419  LVYTQKVAKFSV-ADEMFTMEAKYLLHPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKM 477
                ++ A+      ++       +L  GF  V          +P+ + G L     V  
Sbjct: 1025 AKVLKEKAEVKADGKDVELEALVEILEDGFALV-----YPTRVLPELEKGTL----KVTE 1075

Query: 478  VERKTTPPDYL-TESELISLMEKHGIG---TDASIPVHINNICQRNYVTVTSGRR-LVPT 532
            VE +     YL T+ E++  M++ GIG   T A I   +  + +R YV  + GR+ L+PT
Sbjct: 1076 VEIRKVSKVYLYTQGEVVEEMKERGIGRPSTYAKI---VETLLRRGYVIESKGRKKLIPT 1132

Query: 533  SLGI 536
             LGI
Sbjct: 1133 KLGI 1136

Length = 1187

>gnl|CDD|236048 PRK07561, PRK07561, DNA topoisomerase I subunit omega; Validated

 Score =  114 bits (289), Expect = 1e-26
 Identities = 125/490 (25%), Positives = 194/490 (39%), Gaps = 104/490 (21%)

Query: 100 LANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKT-VWRARFSAITDKDIKA 158
           L   AKD + L L  D D+EGE I + ++E       +      V R  F+ IT   I+ 
Sbjct: 80  LKKAAKDADELYLATDPDREGEAIAWHLLEV------LGGDDVPVKRVVFNEITKNAIQE 133

Query: 159 AMWNLVKP-NIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLD------------- 204
           A  N   P  +     V+A               Q + F      LD             
Sbjct: 134 AFEN---PRELDINL-VNA--------------QQARRF------LDRLVGYMVSPLLWK 169

Query: 205 --ASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLN-------------LNGVA 249
             A  +S G  Q+  +   VER  +I  F PE YW +   L              L+G  
Sbjct: 170 KIARGLSAGRVQSVAVRLIVEREREIEAFVPEEYWDIHADLTTPRGDAFEARLTHLDGKK 229

Query: 250 VSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTK-SKTKPQA-LNTVELMRVASS 307
            +       + +++       A+E  ++ +V  V+   K +  KP A   T  L + AS 
Sbjct: 230 FA----PVDLLNEAQAEAAVAALEGARY-SVASVE--DKPTTRKPSAPFTTSTLQQEASR 282

Query: 308 GLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLS 367
            LG      M+IA+RLY  GY++Y RT++T   +  + +   R      ++G    + L 
Sbjct: 283 KLGFSVKKTMRIAQRLYEAGYITYMRTDSTNLSQ--EAINAARGYIGD-NYGK---KYLP 336

Query: 368 NGISKPR----KGKDVGD-HPPITPTKLATR----TQLDGDAWRLYDYIVRHFIGTLCGD 418
               KPR    K K+  + H  I P+ +         L+GDA RLY+ I + F+ +    
Sbjct: 337 ---EKPRQYSSKAKNAQEAHEAIRPSDVFRTPDQLKGLEGDAQRLYELIWKRFVASQMAP 393

Query: 419 LVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNESI-------PDFKPGDLIP 471
             Y       +  D       + L   GF  V      +++++       P  K GD + 
Sbjct: 394 ARYDSTTVTIAAGDAELRATGRVLRFDGFLKVYV--EGRDDALDDEDRRLPALKVGDALT 451

Query: 472 IQSVKMVERKTTPPDYLTESELISLMEKHGIG---TDASIPVHINNICQRNYVTVTSGRR 528
           ++ +   +  T PP   +E+ L+  +EK GIG   T ASI   I+ I  R YV +   RR
Sbjct: 452 LEKLDPTQHFTKPPARYSEASLVKELEKLGIGRPSTYASI---ISTIQDRGYVRL-ENRR 507

Query: 529 LVPTSLG-IV 537
             P  +G IV
Sbjct: 508 FYPEKMGRIV 517

Length = 859

>gnl|CDD|235840 PRK06599, PRK06599, DNA topoisomerase I; Validated

 Score =  113 bits (286), Expect = 2e-26
 Identities = 125/503 (24%), Positives = 202/503 (40%), Gaps = 97/503 (19%)

Query: 100 LANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAA 159
           L   AK  + + L  D D+EGE I + + E ++        K V R  F+ IT K ++ A
Sbjct: 67  LKKAAKKADAVYLATDPDREGEAIAWHIAEVLK--EAKLKDKNVKRVVFNEITKKAVQEA 124

Query: 160 MWNLVKPNIFEARSVD---ARQELDLRIGCAFTRYQ------TKFFQGKYGDLDASLISY 210
           + N   P   +   VD   AR+ LD  +G     ++       K  +G          S 
Sbjct: 125 IEN---PRDIDMDLVDAQQARRALDYLVG-----FKLSPLLWKKVRRGL---------SA 167

Query: 211 GPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTL-NLNGVAVSVTWS--------RGHIFD 261
           G  Q+  L    ER D+I  F P+ YW ++  L   NG   +            +  I +
Sbjct: 168 GRVQSVALRLICEREDEIEAFIPQEYWTIEADLATSNGEPFTAKLVEVNGKKLEKFSITN 227

Query: 262 KSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAE 321
           +       KA+E  +  TV  ++   + +  P    T  L + AS  LG      M+IA+
Sbjct: 228 EEQAKALVKALEG-QAYTVDKIEKKERKRNPPPPFITSTLQQEASRKLGFSAKKTMRIAQ 286

Query: 322 RLY--------TQGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGI--- 370
           +LY        T G ++Y RT         D V +      S +  D  R+ ++      
Sbjct: 287 KLYEGIDLGEGTVGLITYMRT---------DSVRL------SNEALDEARKYITKKYGKE 331

Query: 371 ---SKPR----KGKDVGD-HPPITPTKLATRT------QLDGDAWRLYDYIVRHFIGTLC 416
              +KPR    K K+  + H  I PT +  RT       L  D ++LY+ I +  + +  
Sbjct: 332 YLPAKPRVYKKKSKNAQEAHEAIRPTSI-NRTPESLKPYLTPDQFKLYELIWKRTVASQM 390

Query: 417 GDLVYTQKVAKFSVADEMFTMEAK--YLLHPGF-----TGVMTWSAMKNESIPDFKPGDL 469
              +  Q     +  +  +   A    +L PGF                + +P  K G+ 
Sbjct: 391 APAILDQTSVDIASENGKYVFRATGSVILFPGFLKVYGESKDDEEEDDEKLLPPLKEGEK 450

Query: 470 IPIQSVKMVERKTTPPDYLTESELISLMEKHGIG---TDASIPVHINNICQRNYVTVTSG 526
           + +  +   +  T PP   +E+ L+  +E++GIG   T ASI   I+ +  R YV +   
Sbjct: 451 LKLDELLPEQHFTEPPPRYSEASLVKKLEEYGIGRPSTYASI---ISTLQDREYVEL-EK 506

Query: 527 RRLVPTSLG-IV---LVHGYQKI 545
           +R +PT LG IV   LV  + K 
Sbjct: 507 KRFIPTDLGRIVNDFLVEHFPKY 529

Length = 675

>gnl|CDD|181555 PRK08780, PRK08780, DNA topoisomerase I; Provisional

 Score =  105 bits (263), Expect = 1e-23
 Identities = 124/488 (25%), Positives = 194/488 (39%), Gaps = 85/488 (17%)

Query: 100 LANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAA 159
           +A  AK  + L L  D D+EGE I + + E ++ +  +   K + R  F+ IT + IK A
Sbjct: 67  IAKAAKSADDLYLATDPDREGEAISWHLAEILKERGLLKD-KPMQRVVFTEITPRAIKEA 125

Query: 160 MWNLVKPNIFEARSVDARQE---LDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTP 216
           M    KP    +  VDA+Q    LD  +G   +    +  Q          +S G  Q+P
Sbjct: 126 M---AKPRDIASDLVDAQQARRALDYLVGFNLSPLLWRKIQ--------RGLSAGRVQSP 174

Query: 217 TLGFCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSR--GHIFDKSTCNVFFKAVEK 274
            L   VER ++I  F    YW ++          +    +  G  F++ T      A   
Sbjct: 175 ALRMIVEREEEIEAFIAREYWSIEADCAHPSQPFNAKLIKLDGQKFEQFTITDGDTAEAA 234

Query: 275 EKHVT--------VVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLY-- 324
              +         V DV+S  + +       T  L + AS  LG      MQ+A++LY  
Sbjct: 235 RLRIQQAAQGTLHVTDVESKERKRNPAPPFTTSTLQQEASRKLGFTTRRTMQVAQKLYEG 294

Query: 325 -------TQGYVSYPRTETTQYPENFDLVAVLRQ-------QESSPDWGDHVREVLSNGI 370
                  + G ++Y RT++    +  D +A +R          S PD             
Sbjct: 295 VDLGDEGSVGLITYMRTDSVNLSQ--DALAEIRDVIARDYGTASLPD------------- 339

Query: 371 SKPR----KGKDVGD-HPPITPTKLATRT------QLDGDAWRLYDYIVRHFIGTLCGDL 419
            +P     K K+  + H  + PT  A RT       L  D  RLY+ I +  +       
Sbjct: 340 -QPNTYKTKSKNAQEAHEAVRPTS-ALRTPAQVARFLSDDQRRLYELIWKRAVACQMIPA 397

Query: 420 VYTQKVAKFSVADE-MFTMEAKYLLHPGFTGVM-----TWSAMKNES---IPDFKPGDLI 470
                    +   E +F      ++ PGF  V        SA   +    +P  K GD +
Sbjct: 398 TLNTVSVDLAAGSEHVFRATGSTVVVPGFLAVYEEGKDDKSAEDEDEGRKLPPMKEGDNV 457

Query: 471 PIQSVKMVERKTTPPDYLTESELISLMEKHGIG---TDASIPVHINNICQRNYVTVTSGR 527
           P++ ++  +  T PP   TE+ L+  +E++GIG   T ASI   I+ +  R YV    GR
Sbjct: 458 PLERIRAEQHFTEPPPRYTEASLVKALEEYGIGRPSTYASI---ISTLQFRKYV-EMEGR 513

Query: 528 RLVPTSLG 535
           R  PT +G
Sbjct: 514 RFRPTDVG 521

Length = 780

>gnl|CDD|236498 PRK09401, PRK09401, reverse gyrase; Reviewed

 Score =  103 bits (260), Expect = 4e-23
 Identities = 110/452 (24%), Positives = 179/452 (39%), Gaps = 87/452 (19%)

Query: 115  DCDKEGENICFEVMEAVRHQININSP--KTVWRARFSAITDKDIKAAMWNL--VKPNIFE 170
            D D EGE I +++   +        P    + R  F  +T K I  A+ N   V  N+ +
Sbjct: 728  DPDTEGEKIAWDLYLLLS-------PYNSNIKRIEFHEVTRKAILEALRNPRDVNENLVK 780

Query: 171  ARSVDARQELDLRIGCAFTRY-QTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIR 229
            A+ V  R+  D  IG   ++  Q KF  GK        +S G  QTP LG+ VER+ + +
Sbjct: 781  AQIV--RRIEDRWIGFELSQKLQKKF--GKRN------LSAGRVQTPVLGWIVERYKEYK 830

Query: 230  TFKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKS 289
              K + Y L+    N  G+ +          +K     F+  + +     V  V+   + 
Sbjct: 831  --KSKGYVLVIKLENGGGLELEGE-----FSEKEEAEKFYNNLIE-----VEKVEEKEEE 878

Query: 290  KTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENFDLVAVL 349
                    T  L+  AS  L +     M+IA+ L+  G ++Y RT++T+       V+  
Sbjct: 879  LNPLPPYTTDTLLSDASRKLRLSAQETMRIAQDLFELGLITYHRTDSTR-------VS-- 929

Query: 350  RQQESSPDWGDHV-----REVLSNGISKPRKGKDVGDHPPITPTKLATRTQL-----DG- 398
                   D G  V      +        PR   + G H  I PT+     +L     +G 
Sbjct: 930  -------DVGISVAKEYLEKRGGEEYFVPRSWGEGGAHEAIRPTRPLDAEELRQMIEEGI 982

Query: 399  ---------DAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEA-KYLLHPGFT 448
                     +  RLYD I R F+ +         +        +   +E    +L  GF 
Sbjct: 983  LKLSEGLTKNHLRLYDLIFRRFMASQMKPAKVRYQKVLIKADGKELELELVVEILEDGFN 1042

Query: 449  GVMTWSAMKNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIG---TD 505
             V+       +  P  +    + ++  K  ++   P    T+ +LIS M++ GIG   T 
Sbjct: 1043 KVLPL-----KLYPLLEGK--VKVKEKKTYKKSKVPL--YTQGDLISEMKERGIGRPSTY 1093

Query: 506  ASIPVHINNICQRNYVTVTSG-RRLVPTSLGI 536
            A I   +  + +R YV  + G +RL+PT LGI
Sbjct: 1094 AKI---VETLLRRGYVIESKGKKRLIPTKLGI 1122

Length = 1176

>gnl|CDD|237803 PRK14724, PRK14724, DNA topoisomerase III; Provisional

 Score = 99.6 bits (248), Expect = 8e-22
 Identities = 124/491 (25%), Positives = 194/491 (39%), Gaps = 81/491 (16%)

Query: 105 KDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNL- 163
           KD   LV   D  +EGE I F ++E           K V R    ++T + I+    NL 
Sbjct: 98  KDVTELVNACDAGREGELI-FRLIEQYAGGAKGGLGKPVKRLWLQSMTPQAIRDGFDNLR 156

Query: 164 ----VKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLG 219
               ++     ARS   R E D  +G   TR  T F     G     L + G  QTPTL 
Sbjct: 157 SDAQMQGLASAARS---RSEADWLVGINGTRAMTAFNSRDGGFF---LTTVGRVQTPTLS 210

Query: 220 FCVERHDKIRTFKPEPYWLLDLTLNLN-----GVAVSVTWSRG---------HIFDKSTC 265
             VER +KIR F    YW +    +       G      W +           ++ +   
Sbjct: 211 LVVEREEKIRKFVSRDYWEIHAGFHAEAGEYLGKWFDPQWKKASDDPEARADRVWSEREA 270

Query: 266 NVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYT 325
                AV + K  TV + +S   ++  P   +   L R A+   G      + +A+ LY 
Sbjct: 271 RAIADAV-RGKAATVTE-ESKPTTQASPLLFDLTSLQREANGKFGFSAKTTLALAQSLYE 328

Query: 326 Q-GYVSYPRTETTQYPEN--------FDLVAVLRQQESSPDWGDHVREVLSNGISKPRK- 375
           +   ++YPRT++   PE+        F+++A    +  +P      ++ L     +P K 
Sbjct: 329 RHKALTYPRTDSRALPEDYLPVAKQTFEMLATSGMRHLAP----FAQQALDGNYVRPSKR 384

Query: 376 ---GKDVGDHPPITPTKLATRTQLDGDAWRLYDYIVRHFIGTLCGDLVY--TQKVAKFSV 430
                 V DH  I PT  A  + L     +LYD +VR F+        Y  T ++++  V
Sbjct: 385 IFDNSKVSDHFAIIPTTQAP-SGLSEAEQKLYDLVVRRFMAVFFPSAEYQVTTRISQ--V 441

Query: 431 ADEMFTMEAKYLLHPGFTGVMTWSAMKNESIPDFKPGD----LIPIQSVKMVER------ 480
               F  E K L+ PG+  +  +       + D K GD    L+P++  +MV        
Sbjct: 442 VGHSFKTEGKVLVKPGWLAI--YGKEAANEVEDAKDGDKGQPLVPVKPGEMVRTEFAEAK 499

Query: 481 --KTTPPDYLTESELISLME----------------KHGIGTDASIPVHINNICQRNYVT 522
             KT PP   +E+ L+  ME                + G+GT A+    I  +    Y+ 
Sbjct: 500 GLKTKPPARYSEATLLGAMESAGKQIDDDELREAMQEKGLGTPATRAAIIEGLLTEKYM- 558

Query: 523 VTSGRRLVPTS 533
           +  GR L+PT+
Sbjct: 559 LREGRELIPTA 569

Length = 987

>gnl|CDD|235778 PRK06319, PRK06319, DNA topoisomerase I/SWI domain fusion protein; Validated

 Score = 83.3 bits (206), Expect = 1e-16
 Identities = 109/492 (22%), Positives = 183/492 (37%), Gaps = 83/492 (16%)

Query: 100 LANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAA 159
           +   AK C+ + L  D D+EGE I + +   +     I       R  F+AIT   +  A
Sbjct: 67  ICKLAKKCDVVYLSPDPDREGEAIAWHIANQLPKNTKIQ------RISFNAITKGAVTEA 120

Query: 160 MWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLG 219
           + +  + ++    +  AR+ LD  +G   +   ++  Q + G      +S G  Q+  L 
Sbjct: 121 LKHPREIDMALVNAQQARRLLDRIVGYKISPILSRKLQRRSG------VSAGRVQSVALK 174

Query: 220 FCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVT------------WSRGHIFDKSTCNV 267
             V+R   I  F P  YW  ++ ++L       T            W +     K+   V
Sbjct: 175 LVVDREKAIEAFVPVEYW--NIRVHLKDPKTQKTFWAHLYSVDGKKWEKEIPEGKTEDEV 232

Query: 268 FF-KAVEKEKHV---------TVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAM 317
               + EK  H+         TV  V+S  K +       T  L + AS          M
Sbjct: 233 LLINSKEKADHIVELLESATYTVTRVESKEKRRNAYPPFITSTLQQEASRHFRFSSSRTM 292

Query: 318 QIAERLY---------TQGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSN 368
            IA+ LY           G ++Y RT++ +               + P+    VR+ +  
Sbjct: 293 NIAQTLYEGVDLDSEGATGLITYMRTDSVR---------------TDPEALKQVRKYIEG 337

Query: 369 GISK---PRKG------KDVGD-HPPITPTKLA-----TRTQLDGDAWRLYDYIVRHFIG 413
              K   P         K   D H  I PT +       R++L  D ++LY  I + F+ 
Sbjct: 338 TFGKEFLPSSPNVYTTKKMAQDAHEAIRPTDITLTPEKLRSKLTEDQYKLYSLIWKRFVA 397

Query: 414 TLCGDLVYTQKVAKFSVADEMFTMEAKYLLH-PGFTGVM------TWSAMKNESIPDFKP 466
           +     +Y     + +    +       LL   GF  V            +N  +P    
Sbjct: 398 SQMIPAIYDTLAIRITTNKGIDLRATGSLLKFKGFLAVYEEKRDDEGDEEENIHLPKLHE 457

Query: 467 GDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSG 526
            D++  + +   +  T P    TE+ L+  +EK GIG  ++    +N I  R Y T+   
Sbjct: 458 QDVLTKEELSAEQAFTKPLPRFTEASLVKELEKSGIGRPSTYATIMNKIQSREY-TLKEN 516

Query: 527 RRLVPTSLGIVL 538
           +RL PT LG ++
Sbjct: 517 QRLRPTELGKII 528

Length = 860

>gnl|CDD|237791 PRK14701, PRK14701, reverse gyrase; Provisional

 Score = 61.4 bits (149), Expect = 9e-10
 Identities = 62/254 (24%), Positives = 98/254 (38%), Gaps = 46/254 (18%)

Query: 319  IAERLYTQGYVSYPRTETTQYPENFDLVAVLRQQ---------ESSPDWGDHVREVLSNG 369
            + ER YT GYV Y  T TT   ENF    ++              S       RE L+  
Sbjct: 1352 VEERYYT-GYV-YDFTTTT---ENFISNGMVSHNCTYHRTDSTRVSNTGIRVAREYLTQE 1406

Query: 370  IS----KPRKGKDVGDHPPITPTK--------------LATRTQLDGDAWRLYDYIVRHF 411
                  KPR     G H  I PT+              +     L  +  RLYD I R F
Sbjct: 1407 NGEDYFKPRDWFMEGAHECIRPTRPIDTDRLIQLIREGIIQVPGLTRNHLRLYDLIFRRF 1466

Query: 412  IGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKN---ESIPDFKPGD 468
            + +            K  +  +   +E +  +     G   WS + +     +P  + G 
Sbjct: 1467 MASQMKP--AKVLYEKALIRYDGKDVEVEGYVEIEGDG---WSRLYSLPLRVLPKLEKGK 1521

Query: 469  LIPIQSVKMVERKTTPPDYL-TESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGR 527
            L     V   + +  P   L T+ ++++LM++ GIG  ++    ++ +  R YV  T GR
Sbjct: 1522 L----KVLEAKIRKAPKVPLYTQGDIVALMKERGIGRPSTYAKIVDTLLMRGYVIETKGR 1577

Query: 528  -RLVPTSLGIVLVH 540
             +L+PT  GI + +
Sbjct: 1578 KKLIPTKKGIKVYN 1591

Length = 1638

>gnl|CDD|173597 PTZ00407, PTZ00407, DNA topoisomerase IA; Provisional

 Score = 58.8 bits (142), Expect = 6e-09
 Identities = 103/519 (19%), Positives = 189/519 (36%), Gaps = 105/519 (20%)

Query: 110 LVLWLDCDKEGENICFEVMEAVRHQI-NINSPKTVWRARFSAITDKDIKAAMWNLVKPNI 168
           ++L  D D+EGE I    ++ ++     +  P +  RA   +IT+  I+ AM        
Sbjct: 128 IILATDPDREGELIAVHALQTIKRLYPKLKVPFS--RAYMHSITEDGIRKAMRER-HVEA 184

Query: 169 FE---ARSVDARQELDLRI----GCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFC 221
            +   A + + R  +D RI    G +  R             ++ + S G  QTP L   
Sbjct: 185 CDYDLANAAETRHAMD-RIFGFLGSSVVRAA-----------NSQMRSIGRVQTPALILI 232

Query: 222 VERHDKIRTF--KPEPYWLLDLTLNLNG-------VAVSVTWSR----GHIFDKSTCNVF 268
            ER DKI+ F    +  + +                 V++T  R     H   ++     
Sbjct: 233 NEREDKIKAFLESNKSTFEVQAMCQFPSPHGTTFSQVVTITPDRKGGASHWATEAEARRC 292

Query: 269 FK--AVEKEKHVTVVDVQSSTKSKTKP-QALNTVELMRVASSGLGMGPHHAMQIAERLYT 325
            +   +      +V        S   P Q       +  A+  L           + L+ 
Sbjct: 293 LEQWKLNNCTGFSVPLEPKPQPSVVPPPQPFTMATAIAKANRQLKYSSEMVSGCLQDLFQ 352

Query: 326 QGYVSYPRTETTQYPENF--DLVAVLRQQ-------------ESSPDWGDHVREVLSNGI 370
            G+++YPRT++T+  E+   D+ A ++++              S+ + G   ++      
Sbjct: 353 LGHITYPRTDSTRIDESALPDIYAAVKKEFGKEFLYRLEDRTVSAQE-GKGSKKTGKKRS 411

Query: 371 SKPRKGKD--VGD----HPPITPTKLATRTQ---LDGDAWRLYDYIVR-----HFIGTLC 416
           +K +KG D  VG+    H  I PT + T  +   L      +YD + R       I    
Sbjct: 412 TKQKKGADTPVGNVEDAHEAIRPTNIDTTGESLSLSPPTRAVYDLVRRNTLAVFMIPMKT 471

Query: 417 GDLVYTQKVAKFSVADEMFTMEAKYLLHPGFT--------GVMTWSAMKNESIPDFKPGD 468
             +V T K    S     F ++ K ++ PG+T        G    +   +E I   + G 
Sbjct: 472 EKIVATVKFTSGSGEKLEFELQGKRVVEPGWTRAFHKGDKGTTGPAEETDEDITAVEEGA 531

Query: 469 LI----------------------------PIQSVKMVERKTTPPDYLTESELISLMEKH 500
            +                             ++S ++ E +  PP   +E  LI  ++ +
Sbjct: 532 PVVPSLSQEEFKAIMNLRSQLGSGVQKGFFELRSPQVRENRPVPPLPHSEGTLIEELKNN 591

Query: 501 GIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLV 539
           G+G  ++ P+ +  +  R Y+ V    R   T +G +LV
Sbjct: 592 GVGRPSTYPMIVKTLLARGYIAVNPKGRCETTPVGRMLV 630

Length = 805

>gnl|CDD|237791 PRK14701, PRK14701, reverse gyrase; Provisional

 Score = 48.7 bits (116), Expect = 8e-06
 Identities = 52/235 (22%), Positives = 96/235 (40%), Gaps = 41/235 (17%)

Query: 104 AKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSP--KTVWRARFSAITDKDIKAAMW 161
           A + + +++  D D EGE I +++        N+ +P    + R  F  +T + I  A+ 
Sbjct: 698 AHEVDEILIGTDPDTEGEKIAWDIR-------NVLAPYGPNIKRIEFHEVTRRAILKAIK 750

Query: 162 NL--VKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLG 219
               +  N  +A+ V  R+  D  IG   ++   + F+ +        +S G  QTP LG
Sbjct: 751 EARDIDENRVKAQIV--RRIEDRWIGFELSQKLWEVFEDRN-------LSAGRVQTPVLG 801

Query: 220 FCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVT 279
           + ++R+ +   F       L + L  N + V++  S+                  E  V 
Sbjct: 802 WIIQRYKE---FTESKVPFLGIILE-NDLTVTIEDSKD-----------------EVEVE 840

Query: 280 VVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRT 334
           V  V+   K +       T  ++R AS+ L +     M++A+ L+  G    P T
Sbjct: 841 VELVEEEEKERNPLPPYTTDTMLRDASAFLKLSAKETMKLAQDLFEAGLCVTPDT 895

Length = 1638

>gnl|CDD|173783 cd03363, TOPRIM_TopoIA_TopoI, TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to Escherichia coli DNA topoisomerase I

 Score = 42.5 bits (101), Expect = 6e-05
 Identities = 30/106 (28%), Positives = 41/106 (38%), Gaps = 12/106 (11%)

Query: 57  CGHIMGLDFTSKYNNWDKVDPLELFSCPTEKREATPKLKLPAFLANEAKDCEFLVLWLDC 116
            GHI  L           VD  +    P        K K+   L   AK  + + L  D 
Sbjct: 29  VGHIRDLPKKGLG-----VDGEDDGFEPKYVVIPG-KKKVVKELKKLAKKADEIYLATDP 82

Query: 117 DKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWN 162
           D+EGE I + + E       +   K V R  F+ IT + IK A+ N
Sbjct: 83  DREGEAIAWHLAEV------LKLKKNVKRVVFNEITKEAIKEALKN 122

Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. Length = 123

>gnl|CDD|214695 smart00493, TOPRIM, topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins

 Score = 38.8 bits (91), Expect = 4e-04
 Identities = 13/41 (31%), Positives = 21/41 (51%), Gaps = 1/41 (2%)

Query: 93  KLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRH 133
             +    L   AK  E ++L  D D+EGE I +E+ E ++ 
Sbjct: 34  SKEQIKLLKKLAKKAE-VILATDPDREGEAIAWELAELLKP 73

Length = 75

>gnl|CDD|216679 pfam01751, Toprim, Toprim domain

 Score = 36.9 bits (86), Expect = 0.003
 Identities = 18/107 (16%), Positives = 34/107 (31%), Gaps = 37/107 (34%)

Query: 45  FGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPTEKREATPKLKLPAFLANEA 104
            G ++   + +  GH + L                              +K    L    
Sbjct: 17  AGGVLGGAVVATSGHALDL----------------------------EHIKE---LKKAL 45

Query: 105 KDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAI 151
           K  + ++L  D D+EGE I  +++E ++    I       R   S +
Sbjct: 46  KGAKEVILATDPDREGEAIALKLLELLKPLGPIG------RVEISEL 86

This is a conserved region from DNA primase. This corresponds to the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR proteins. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase EC:2.7.7.6 is a nucleotidyltransferase it synthesises the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases. Type II DNA topoisomerases catalyze the relaxation of DNA supercoiling by causing transient double strand breaks. Length = 86

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	562
PRK07220	740	DNA topoisomerase I; Validated	100.0
PRK08173	862	DNA topoisomerase III; Validated	100.0
PRK05776	670	DNA topoisomerase I; Provisional	100.0
PRK14973	936	DNA topoisomerase I; Provisional	100.0
TIGR01057	618	topA_arch DNA topoisomerase I, archaeal. This mode	100.0
PRK07219	822	DNA topoisomerase I; Validated	100.0
PRK14724	987	DNA topoisomerase III; Provisional	100.0
COG0550	570	TopA Topoisomerase IA [DNA replication, recombinat	100.0
TIGR01056	660	topB DNA topoisomerase III, bacteria and conjugati	100.0
PRK07726	658	DNA topoisomerase III; Provisional	100.0
TIGR01051	610	topA_bact DNA topoisomerase I, bacterial. This mod	100.0
PRK05582	650	DNA topoisomerase I; Validated	100.0
PRK08780	780	DNA topoisomerase I; Provisional	100.0
PRK07561	859	DNA topoisomerase I subunit omega; Validated	100.0
PRK06599	675	DNA topoisomerase I; Validated	100.0
PRK06319	860	DNA topoisomerase I/SWI domain fusion protein; Val	100.0
PTZ00407	805	DNA topoisomerase IA; Provisional	100.0
PRK09401	1176	reverse gyrase; Reviewed	100.0
KOG1956|consensus	758		100.0
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	100.0
PF01131	403	Topoisom_bac: DNA topoisomerase; InterPro: IPR0134	100.0
cd00186	381	TOP1Ac DNA Topoisomerase, subtype IA; DNA-binding,	100.0
PRK14701	1638	reverse gyrase; Provisional	100.0
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	100.0
KOG1957|consensus	555		100.0
smart00437	259	TOP1Ac Bacterial DNA topoisomerase I DNA-binding d	100.0
cd03362	151	TOPRIM_TopoIA_TopoIII TOPRIM_TopoIA_TopoIII: The t	100.0
cd01028	142	TOPRIM_TopoIA TOPRIM_TopoIA: topoisomerase-primase	100.0
smart00436	89	TOP1Bc Bacterial DNA topoisomeraes I ATP-binding d	99.97
cd03361	170	TOPRIM_TopoIA_RevGyr TopoIA_RevGyr : The topoisome	99.96
cd03363	123	TOPRIM_TopoIA_TopoI TOPRIM_TopoIA_TopoI: The topoi	99.96
PF01751	100	Toprim: Toprim domain; InterPro: IPR006171 This is	99.81
cd01025	112	TOPRIM_recR TOPRIM_recR: topoisomerase-primase (TO	97.95
smart00493	76	TOPRIM topoisomerases, DnaG-type primases, OLD fam	97.89
PRK00076	196	recR recombination protein RecR; Reviewed	96.57
cd01027	81	TOPRIM_RNase_M5_like TOPRIM_ RNase M5_like: The to	96.09
cd00188	83	TOPRIM Topoisomerase-primase domain. This is a nuc	95.79
smart00437	259	TOP1Ac Bacterial DNA topoisomerase I DNA-binding d	92.3
PF13662	81	Toprim_4: Toprim domain; PDB: 1EQN_E 1DD9_A 3B39_B	92.13
PRK13844	200	recombination protein RecR; Provisional	91.5
TIGR01057	618	topA_arch DNA topoisomerase I, archaeal. This mode	91.03
PF01131	403	Topoisom_bac: DNA topoisomerase; InterPro: IPR0134	91.02
TIGR00615	195	recR recombination protein RecR. This family is ba	90.51
COG1658	127	Small primase-like proteins (Toprim domain) [DNA r	89.6
TIGR00334	174	5S_RNA_mat_M5 ribonuclease M5. This family of orth	88.89
COG4026	290	Uncharacterized protein containing TOPRIM domain,	88.76
PRK04031	408	DNA primase; Provisional	88.4
PRK07220	740	DNA topoisomerase I; Validated	88.25
COG0353	198	RecR Recombinational DNA repair protein (RecF path	86.02
COG0550	570	TopA Topoisomerase IA [DNA replication, recombinat	85.96
cd00186	381	TOP1Ac DNA Topoisomerase, subtype IA; DNA-binding,	85.84
TIGR01051	610	topA_bact DNA topoisomerase I, bacterial. This mod	85.5
PRK05776	670	DNA topoisomerase I; Provisional	85.46
PRK07219	822	DNA topoisomerase I; Validated	85.37
PF14947	77	HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_	84.38
smart00529	96	HTH_DTXR Helix-turn-helix diphteria tox regulatory	84.27
COG3432	95	Predicted transcriptional regulator [Transcription	82.43
TIGR01056	660	topB DNA topoisomerase III, bacteria and conjugati	81.59
PRK08173	862	DNA topoisomerase III; Validated	81.18
PF08259	11	Periviscerokin: Periviscerokinin family; InterPro:	80.79
PRK11512	144	DNA-binding transcriptional repressor MarR; Provis	80.58
PRK14973	936	DNA topoisomerase I; Provisional	80.32
PRK05582	650	DNA topoisomerase I; Validated	80.32
PF07848	70	PaaX: PaaX-like protein; InterPro: IPR012906 This	80.31

>PRK07220 DNA topoisomerase I; Validated

Probab=100.00  E-value=2.8e-131  Score=1118.92  Aligned_cols=532  Identities=30%  Similarity=0.522  Sum_probs=469.0

Q ss_pred             eEEEEecccCcCCcchHHhhcccccCCC-------CceeeeeeeeEcCCCcEEEEEEecccccccccccCCCCCccCCCC
Q psy8714           6 KKLVPASEIKLARPSLISLLTPLQRMNG-------ACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPL   78 (562)
Q Consensus         6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~-------~~~~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~~~~y~~W~~~~p~   78 (562)
                      |+||||||     ||+|+.||+++|..+       .+++|+|.  .+|+  .|+|+||.|||++|++|++|+.|..+++.
T Consensus         1 m~LiIaEK-----Ps~Ak~Ia~~Lg~~~~~~~~~~g~~~y~~~--~~g~--~~~v~~~~GHl~~l~~P~~y~~w~~~~~~   71 (740)
T PRK07220          1 MHLIITEK-----NIAARRIAQILAPKKPKKTRVSGVDVYRYE--DNGD--DTVVVGLSGHIVNIDFPKEYNNWQKVDAR   71 (740)
T ss_pred             CeEEEEeC-----HHHHHHHHHHhCCCCccccccCCcceeEEe--cCCC--CEEEEEeCcccccCCCCccccccCCCChh
Confidence            57999999     999999999998321       22234332  1354  48899999999999999999889887776


Q ss_pred             CCCCCCcccccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHH
Q psy8714          79 ELFSCPTEKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKA  158 (562)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~  158 (562)
                      .+|+.+....  ..+.++++.|++++++||+||||||||||||+|||||+++++..   +++++++|+|||++|+++|++
T Consensus        72 ~l~~~~~~~~--~~~~~~~~~lk~l~k~ad~viiAtD~DREGE~I~~~i~~~l~~~---~~~~~~~R~~fs~iT~~~I~~  146 (740)
T PRK07220         72 DLIDAEIITT--PTQKKIVTALKKLGKEADRVTIATDYDREGELIGVEALNIIKKV---NPDIKFDRVRYSAITKKEIER  146 (740)
T ss_pred             HcCCcceEec--CCHHHHHHHHHHHHhcCCEEEECCCCCccHHHHHHHHHHHHHhc---CCCCceEEEEEccCCHHHHHH
Confidence            6664332211  23457889999999999999999999999999999999999753   345799999999999999999


Q ss_pred             HHHhCCCChHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhhhhhhhhhhcccCcceEE
Q psy8714         159 AMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWL  238 (562)
Q Consensus       159 A~~nl~~~~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lIv~Re~eI~~F~p~~y~~  238 (562)
                      ||+||+++|.++++||+|||++||||||||||++|+.+++. +   ++++|+||||||||+|||+||+||+||+|++||+
T Consensus       147 A~~n~~~~d~~l~~A~~aR~~~D~lvG~nlSr~~t~~~~~~-~---~~~lS~GRVQtptL~lIv~Re~eI~~F~p~~y~~  222 (740)
T PRK07220        147 AFSNPVEVDFNLADAGHSRQVIDLVWGAALTRYISLAAGRL-G---KMFLSVGRVQSPTLALIVDREKEREAFVPTPYWE  222 (740)
T ss_pred             HHhCCCCCChhHHHHHHHHHHHHHHhchhcCHHHHHHHHhh-C---CccccccccchhhhHHHHhhHHHHHhCCCCccEE
Confidence            99999999999999999999999999999999999877532 1   2369999999999999999999999999999999


Q ss_pred             EEEEEeeCCeEEEEEeecccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHHHHHHHHHhhCCCCHHHHHH
Q psy8714         239 LDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQ  318 (562)
Q Consensus       239 i~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl~  318 (562)
                      |.+.+..++..|.+.|..++++|+++|+++++.+ + +.++|++|+.++++.+||+||||++||++||+ +||||++||+
T Consensus       223 i~~~~~~~~~~~~~~~~~~r~~~~~~a~~~~~~~-~-~~~~V~~v~~~~~~~~pP~pf~ts~Lq~~a~~-~g~s~~~tm~  299 (740)
T PRK07220        223 IYATLENNGETFVAQHSTRRFWEKEEADRVFEKL-G-KTAEVTEVEKGTKTDKPPTPFNTTEFISAANS-IGFSAANAMR  299 (740)
T ss_pred             EEEEEEcCCceEEEEeccCcCCCHHHHHHHHHhh-C-CCeEEEEEeeeeEecCCCCCcCHHHHHHHHHH-cCCCHHHHHH
Confidence            9999987778899999888999999999999998 3 47999999999999999999999999999995 8999999999


Q ss_pred             HHHHhHhcCceeecCCCCCCCCCcccHHHHHHHhccCCchhHHHHHHhhCCCCCCCC-CCCCCCCCCCccCCCcccCCCC
Q psy8714         319 IAERLYTQGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRK-GKDVGDHPPITPTKLATRTQLD  397 (562)
Q Consensus       319 iaQ~LYE~glISYPRTds~~l~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~H~AI~PT~~~~~~~L~  397 (562)
                      +||+|||+||||||||||++||+++++..+++.+.. ..|+.++..++..+...|.. .++++||||||||...+.+.|+
T Consensus       300 iaQ~LYe~g~ITYPRTDs~~l~~~~~~~~~i~~l~~-~~~~~~~~~~l~~~~~~~~~~~~~~~~H~aI~PT~~~~~~~L~  378 (740)
T PRK07220        300 IAESLYTNGYISYPRTDNTVYPESLDLREQIEIFAE-GPFGEYAQKLLEKGELVPTRGKKETTDHPPIYPASLAKKSELK  378 (740)
T ss_pred             HHHHHHhCCceeecccCCeecCchhhHHHHHHHHHH-HHHHHHHHHhcccCCccCCCCCCCCCCCCCCCcccCCCcccCC
Confidence            999999999999999999999998888888887754 24666665555433223333 3456899999999986556899


Q ss_pred             HHHHHHHHHHHHHHHhhcccCceEEEEEEEEEECCeEEEEEEEEEeecceeeeecccccccCCCCCCCCCCeeeeeeeEE
Q psy8714         398 GDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKM  477 (562)
Q Consensus       398 ~~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~v~~~~~~~~~~Lp~l~~G~~~~~~~~~i  477 (562)
                      ++|++||+||||||||+||+||+|++|+|.++++++.|+++|++++++||++||+++..++..||.+++||.+.+.++.+
T Consensus       379 ~de~~lY~LI~rRfla~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~vy~~~~~~~~~LP~l~~Ge~~~~~~~~~  458 (740)
T PRK07220        379 EDEWKVYELVVRRFFATFAGPAEWETMKLRFDIGGEEFRANGSRLTEPGWRWYYPYNAPEDRLLPELSEGEELKVKKKEM  458 (740)
T ss_pred             HHHHHHHHHHHHHHHHHhCchheEEEEEEEEEECCeEEEEeeeEEeeCChHHHcCccccccccCCCCCCCCEeeeeeeee
Confidence            99999999999999999999999999999999999999999999999999999976544456799999999999999999


Q ss_pred             eeeecCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEcCCCeeecchhHHHHHHhhhccCccCCChhhHHH
Q psy8714         478 VERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSA  557 (562)
Q Consensus       478 ~e~~TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~~~k~l~~T~~G~~li~~l~~~~~~l~~p~~Ta~  557 (562)
                      .+++|+||+||||++||++||+.|||||||||+||++|++||||+   |+.|+||++|+.|+++|....+.|++|+|||.
T Consensus       459 ~ek~TkPP~ryTea~Li~~Me~~GIGTpATra~iI~~L~~R~Yi~---~k~l~pT~~G~~v~~~l~~~~~~i~~~~~Ta~  535 (740)
T PRK07220        459 LDKETQPPGRYGQGRLIKLMEDLGLGTKATRHEIISKLYSRAYIH---GNPIQPTNTAFAVVDALEKYAPTITKPDMTSR  535 (740)
T ss_pred             cccccCCCCCCCHHHHHHHHHhCCCCCCCcHHHHHHHHHhcCCcc---CCcccccHHHHHHHHHHHHhchhhcChhHHHH
Confidence            999999999999999999999999999999999999999999996   46899999999999999888889999999999


Q ss_pred             HHhhC
Q psy8714         558 YRVQA  562 (562)
Q Consensus       558 ~E~~L  562 (562)
                      ||.+|
T Consensus       536 ~E~~L  540 (740)
T PRK07220        536 LEEDM  540 (740)
T ss_pred             HHHHH
Confidence            99876

>PRK08173 DNA topoisomerase III; Validated

Probab=100.00  E-value=5.8e-131  Score=1126.10  Aligned_cols=530  Identities=24%  Similarity=0.386  Sum_probs=453.2

Q ss_pred             eEEEEecccCcCCcchHHhhcccccCCCCceeeeeeeeEcCCCcEEEEEEecccccccccccCC----CCCccCCCCCCC
Q psy8714           6 KKLVPASEIKLARPSLISLLTPLQRMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKY----NNWDKVDPLELF   81 (562)
Q Consensus         6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~~~~~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~~~~y----~~W~~~~p~~~~   81 (562)
                      |+||||||     ||+|+.||.++|..+.     -+|||+|++  |+||||+|||++|..|++|    ++|+..++. ++
T Consensus         3 ~~LiIAEK-----Ps~Ak~Ia~~Lg~~~k-----~~gy~e~~~--~~Vtwa~GHL~el~~Pe~Y~~~~~~W~~~~LP-i~   69 (862)
T PRK08173          3 KALIIAEK-----PSVANDIARALGGFTK-----HDEYFESDE--YVLSSAVGHLLEIAAPEEYEVKRGKWSFAHLP-VI   69 (862)
T ss_pred             CEEEEEeC-----HHHHHHHHHHhCCCcC-----CCCeEeCCc--EEEEeeccccccCCCchhcccccccccccccC-CC
Confidence            46999999     9999999999976543     378999874  8999999999999877765    578765521 22


Q ss_pred             CCCc---ccccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHH
Q psy8714          82 SCPT---EKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKA  158 (562)
Q Consensus        82 ~~~~---~~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~  158 (562)
                      +.+.   ......+|+++|+.|.+. ++||+||||||||||||+|+|+|+++++      +++||+|+||||||+++|++
T Consensus        70 p~~f~~~~~~~~~~q~~~ik~l~k~-~~~d~Ii~AtD~dREGElI~~~I~~~~~------~~kpv~Rlw~sslt~~aI~~  142 (862)
T PRK08173         70 PPHFDLNPIAKTESRLKVLTKLIKR-KDVTRLINACDAGREGELIFRLIAQHAK------AKKPVKRLWLQSMTPQAIRD  142 (862)
T ss_pred             CccccccccccHHHHHHHHHHHHhh-CCCCEEEECCCCChhHHHHHHHHHHHhC------CCCCeEEEEEccCCHHHHHH
Confidence            2111   112222344444444321 5799999999999999999999999994      46899999999999999999


Q ss_pred             HHHhCCCCh--HhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhhhhhhhhhhcccCcce
Q psy8714         159 AMWNLVKPN--IFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPY  236 (562)
Q Consensus       159 A~~nl~~~~--~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lIv~Re~eI~~F~p~~y  236 (562)
                      ||+||++++  .++++||.||+++|||||||+||++|+..+.. |.  ..++|+||||||||+|||+||++|+||+|++|
T Consensus       143 a~~nl~~~~~~~~L~~aa~aR~~aDwlvG~N~TR~~T~~~~~~-g~--~~~lSvGRVQTPtL~lVv~Re~eI~~F~p~~y  219 (862)
T PRK08173        143 GFANLRSDEDMQPLADAARCRSEADWLVGINGTRAMTAFNSKG-GG--FFLTTVGRVQTPTLSIVVEREEKIRRFVPRDY  219 (862)
T ss_pred             HHhcCCCchhhHHHHHHHHHHHHHHHHhhHHHhHHHHHhHhhc-CC--ccccccccchhhHHHHHHHHHHHHHcCCCCcc
Confidence            999999987  48999999999999999999999999854432 21  24689999999999999999999999999999


Q ss_pred             EEEEEEEeeCCeEEEEEee--------------cccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHHHHH
Q psy8714         237 WLLDLTLNLNGVAVSVTWS--------------RGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELM  302 (562)
Q Consensus       237 ~~i~~~~~~~~~~~~~~~~--------------~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq  302 (562)
                      |+|.+.+...++.|.+.|.              .++++|+++|+.+++.|.+ ++++|++ +.+++++.||+||||++||
T Consensus       220 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~d~~~A~~i~~~~~~-~~~~V~~-~~k~~~~~pP~~f~Lt~LQ  297 (862)
T PRK08173        220 WEVRAEFVAAAGFYEGRWFDPKFKKDEFDPEKRASRLWSEAAAEAIVAACRG-KPGTVTE-ESKPSTQLSPLLFDLTSLQ  297 (862)
T ss_pred             EEEEEEEecCCccEEEEEeccccccccccccccccccCCHHHHHHHHHHhcC-CCcEEEE-eeeEEecCCCCCCCHHHHH
Confidence            9999999877777888883              2589999999999999986 4789988 8899999999999999999


Q ss_pred             HHHHhhCCCCHHHHHHHHHHhHhc-CceeecCCCCCCCCCcc--cHHHHHHHhccCCchhHHHHHHhhCCC--CCCC--C
Q psy8714         303 RVASSGLGMGPHHAMQIAERLYTQ-GYVSYPRTETTQYPENF--DLVAVLRQQESSPDWGDHVREVLSNGI--SKPR--K  375 (562)
Q Consensus       303 ~~a~~~~g~s~~~tl~iaQ~LYE~-glISYPRTds~~l~~~~--~~~~~l~~l~~~~~~~~~~~~~~~~~~--~~~~--~  375 (562)
                      ++||++|||||++||++||+|||+ |+||||||||+|||+++  ++..+|+.+...+.+..++..++....  ...+  +
T Consensus       298 ~~A~~~~g~sa~~tL~iaQ~LYE~~k~iTYPRTDs~~l~~~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~r~~~  377 (862)
T PRK08173        298 REANGRFGFSAKNTLGLAQALYEKHKVLTYPRTDSRALPEDYLGTVKQTLEMLKESNNYLPHAKQILDKGWVKPNKRIFD  377 (862)
T ss_pred             HHHHHhcCCCHHHHHHHHHHHHhcCCEEEecCCCCccCCHHHHHHHHHHHHHHhCCcccHHHHHHhhcccccCCCCCcCC
Confidence            999999999999999999999996 89999999999999986  578888888654456655554443221  1223  2


Q ss_pred             CCCCCCCCCCccCCCcccCCCCHHHHHHHHHHHHHHHhhcccCceEEEEEEEEEECCeEEEEEEEEEeecceeeeecccc
Q psy8714         376 GKDVGDHPPITPTKLATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSA  455 (562)
Q Consensus       376 ~~~~~~H~AI~PT~~~~~~~L~~~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~v~~~~~  455 (562)
                      .++++||||||||...+ ..|+++|++||+||+|||||+|||||+|+.|+|.+.++++.|+++|++++++||+.||+.+.
T Consensus       378 ~~kv~dH~AIiPT~~~~-~~Ls~~E~~iY~lI~rRfla~f~~~a~~~~t~v~~~v~~~~F~a~G~~~~~~Gw~~vy~~~~  456 (862)
T PRK08173        378 NSKISDHFAIIPTLQAP-KSLSEPEQKLYDLVVKRFLAVFFPAAEFLVTTRITEVAGHHFKTEGKVLVNPGWLAVYGKEA  456 (862)
T ss_pred             CCCCCCCCCcCccCCCc-ccCCHHHHHHHHHHHHHHHHHhCchheEEEEEEEEEeCCcEEEEEEEEEeeCChHHHhCccc
Confidence            45578999999998765 46999999999999999999999999999999999999999999999999999999997543


Q ss_pred             c-ccCCCCCCCCCCeeeeeeeEEeeeecCCCCCCCHHHHHHHHH----------------hcCCCCcCchhHHHHHhhcC
Q psy8714         456 M-KNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLME----------------KHGIGTDASIPVHINNICQR  518 (562)
Q Consensus       456 ~-~~~~Lp~l~~G~~~~~~~~~i~e~~TkPP~~~Te~~Li~~Me----------------~~GIGTpATra~iI~~L~~r  518 (562)
                      . ++..||.|++||.+.+.++.+.+++|+||+||||++||++||                +.|||||||||+||++|++|
T Consensus       457 ~~~~~~LP~l~~Ge~~~~~~~~~~e~~TkPP~ryTEatLl~aMe~~gk~v~D~el~~~~~~~GIGTpATRA~IIe~L~~r  536 (862)
T PRK08173        457 QGADANLVPVQKGEKVKTDKIEAVALTTKPPARYNEATLLSAMEGAGKLVEDDELREAMAEKGLGTPATRAAIIEGLLGE  536 (862)
T ss_pred             ccccccCCCcCCCCEeeeeeeeecccccCCCCCcCHHHHHHHHHhhhhccccHHHHhhhhcCCCCchhhHHHHHHHHHhC
Confidence            2 245699999999999999999999999999999999999998                57999999999999999999


Q ss_pred             CeEEEcCCCeeecchhHHHHHHhhhcc-CccCCChhhHHHHHhhC
Q psy8714         519 NYVTVTSGRRLVPTSLGIVLVHGYQKI-DRELVEPTMRSAYRVQA  562 (562)
Q Consensus       519 ~Yi~~~~~k~l~~T~~G~~li~~l~~~-~~~l~~p~~Ta~~E~~L  562 (562)
                      |||++ +|+.|+||++|+.||++|... ++.|++|+|||.||.+|
T Consensus       537 ~Yi~~-~~k~l~pT~~G~~li~~l~~~~~~~l~~p~lTa~wE~~L  580 (862)
T PRK08173        537 KYLVR-EGRELIPTAKAFQLMTLLRGLGVEELTSPELTGEWEYKL  580 (862)
T ss_pred             CcEEe-cCCEechhHHHHHHHHHHhhcCcccccChhHHHHHHHHH
Confidence            99997 678999999999999998653 56799999999999976

>PRK05776 DNA topoisomerase I; Provisional

Probab=100.00  E-value=2.7e-130  Score=1097.80  Aligned_cols=534  Identities=25%  Similarity=0.410  Sum_probs=465.6

Q ss_pred             eEEEEecccCcCCcchHHhhcccccCCC-CceeeeeeeeEc----CCCcEEEEEEecccccccccccC-CCCCcc-CCCC
Q psy8714           6 KKLVPASEIKLARPSLISLLTPLQRMNG-ACSVHEWVGPLF----GDLVLFKMTSVCGHIMGLDFTSK-YNNWDK-VDPL   78 (562)
Q Consensus         6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~-~~~~~~~~g~~~----g~~~~~~Vt~~~GHl~~l~~~~~-y~~W~~-~~p~   78 (562)
                      |.||||||     ||+|+.||+++|... .... ...|||+    |.  .|+|+||.|||++|++|+. |..+.. +.| 
T Consensus         2 ~~LiIaEK-----Ps~Ak~Ia~~Lg~~~~~~~~-~g~~~~e~~~~g~--~~~V~~~~GHl~~L~~~~~~~~~~~~~~~p-   72 (670)
T PRK05776          2 YILVIAEK-----PKAARKIAEALSEKPIRCRI-YGVPYWIVKRDGK--KIVVAPAAGHLFGLHTKSKGFPVFDYEWKP-   72 (670)
T ss_pred             CEEEEEcC-----HHHHHHHHHHhCCCcccccc-CCCceEEEecCCC--CEEEEEecccCccCCCcccCCCCCCcCccc-
Confidence            68999999     999999999998321 1111 1124454    54  4899999999999987763 321110 112 


Q ss_pred             CCCCCCcccccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHH
Q psy8714          79 ELFSCPTEKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKA  158 (562)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~  158 (562)
                       .|.....   .....++++.|++++++||+||||||||||||+|||||+++++      +.++++|+|||++|+++|++
T Consensus        73 -~~~~~~~---~~~~~~~~~~lk~l~k~ad~iiiAtD~DREGE~I~~~i~~~~~------~~~~v~R~~fs~iT~~~I~~  142 (670)
T PRK05776         73 -LYEIDKG---SKYTKKYYELLSSLSKYADEFINACDYDIEGSVIGYLIIKYLG------DPKKAKRMKFSALTKSDIRR  142 (670)
T ss_pred             -ceEeccC---cccHHHHHHHHHHHHhcCCEEEECCCCChhHHHHHHHHHHHhC------CCCCeeEEEEccCCHHHHHH
Confidence             2221111   0112368889999999999999999999999999999999995      25799999999999999999


Q ss_pred             HHHhCCCChHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhhhhhhhhhhcccCcceEE
Q psy8714         159 AMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWL  238 (562)
Q Consensus       159 A~~nl~~~~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lIv~Re~eI~~F~p~~y~~  238 (562)
                      ||+||+++|.++++||+||+++|||||||+||++|+.++...|.  ..++|+||||||||+|||+||+||++|+|++||.
T Consensus       143 A~~n~~~~d~~l~~A~~aR~~lD~lvG~nlSr~lt~~~~~~~g~--~~~lS~GRVQsptL~lVveRe~eI~~Fvp~~yw~  220 (670)
T PRK05776        143 AFRNLETLDYEMINAGIARHELDWLWGINVSRALMSSVRDASGK--RVILSAGRVQSPTLKYVVEREIERNLFVPLPYFS  220 (670)
T ss_pred             HHhCccccchhHHHHHHHHHHHHHHHhHHHhHHHHHHhhhhcCC--ccceecceecCchhhHhHhhHHHHHcCCCCcceE
Confidence            99999999999999999999999999999999999887643221  2479999999999999999999999999999999


Q ss_pred             EEEEEeeCCeEEEEEeecccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHHHHHHHHHhhCCCCHHHHHH
Q psy8714         239 LDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQ  318 (562)
Q Consensus       239 i~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl~  318 (562)
                      |.+.+..++..|.+.|...++.|+++|+++++.+++.+.++|.+|+.++++.+||+||||++||++||++|||||++||+
T Consensus       221 i~~~~~~~~~~f~~~~~~~~~~~~~~a~~i~~~~~~~~~~~V~~v~~k~~~~~pP~pf~ts~LQ~~As~~lg~sa~ktm~  300 (670)
T PRK05776        221 VSIIIEKNGYEFTLKYENKKFETKEEAKEILEEIKKTGYLKVTKVEVKIEILEPPPPFNLGDLQVEAARIYGFSPYKTQS  300 (670)
T ss_pred             EEEEEecCCceEEEEEcCCccCCHHHHHHHHHHhcCCCCEEEEEEEeeeEEcCCCCCCCHHHHHHHHHhhcCCCHHHHHH
Confidence            99999877888999998788999999999999997645799999999999999999999999999999999999999999


Q ss_pred             HHHHhHhcCceeecCCCCCCCCCcccHHHHHHHhccCCchhHHHHHHhhC--CCCCCCCCCCC-CCCCCCccCCCcccCC
Q psy8714         319 IAERLYTQGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSN--GISKPRKGKDV-GDHPPITPTKLATRTQ  395 (562)
Q Consensus       319 iaQ~LYE~glISYPRTds~~l~~~~~~~~~l~~l~~~~~~~~~~~~~~~~--~~~~~~~~~~~-~~H~AI~PT~~~~~~~  395 (562)
                      +||+|||+||||||||||++||+++++.++++.+...+.|+.++..++..  ...+|+++.+. +||||||||+..+ .+
T Consensus       301 iAQ~LYe~glISYPRTDs~~ls~~~~~~~~~~~l~~~~~~~~~~~~~l~~~~~~~~~~~~~k~~~aH~AI~PT~~~p-~~  379 (670)
T PRK05776        301 IAEDLYLDGLISYPRTNSQKLPPTLNIRNILKGLSRSPQYRPLVNLLLKETKGVLKPVQGPKDDPAHPAIYPTGEPP-KN  379 (670)
T ss_pred             HHHHHHhcCceecCCCccCCCChhhCHHHHHHHHhcchhHHHHHHHhhcccCCccccCCCCCCCCCCCCCCCCCCCc-cc
Confidence            99999999999999999999999988888999888777788877666542  23345555544 5899999998754 57


Q ss_pred             CCHHHHHHHHHHHHHHHhhcccCceEEEEEEEEEECCe--EEEEEEEEEeecceeeeecccccccCCCCCCCCCCeeeee
Q psy8714         396 LDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADE--MFTMEAKYLLHPGFTGVMTWSAMKNESIPDFKPGDLIPIQ  473 (562)
Q Consensus       396 L~~~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~~--~F~a~g~~~~~~Gw~~v~~~~~~~~~~Lp~l~~G~~~~~~  473 (562)
                      |+++|++||+||||||||+||+||+|++|+|.+.++++  .|+++|++++++||+.||+++++++..||.|++||.+.+.
T Consensus       380 L~~de~klY~LI~rRflA~~~~~a~~~~t~v~~~~~~~~~~F~a~G~~i~~~Gw~~vy~~~~~~~~~LP~l~~G~~~~~~  459 (670)
T PRK05776        380 LSKDEFKLYDLIVRRFLASFAAPAVLSNTIVTLRVPGFPLVFSASGQRIEERGWLKYYPFHKFDEEELPLLKKGERVKIV  459 (670)
T ss_pred             CCHHHHHHHHHHHHHHHHHhChhheEEEEEEEEEECCeEEEEEEEEEEEEECCceeecccCccccccCCCcCCCCEeEee
Confidence            99999999999999999999999999999999999999  9999999999999999997655445679999999999999


Q ss_pred             eeEEeeeecCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEcCCCeeecchhHHHHHHhhhccCccCCChh
Q psy8714         474 SVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPT  553 (562)
Q Consensus       474 ~~~i~e~~TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~~~k~l~~T~~G~~li~~l~~~~~~l~~p~  553 (562)
                      ++.+.+++|+||+||||++||++||+.|||||||||+||++|++||||.+ +|+.|+||++|+.|+++|...++.|++|+
T Consensus       460 ~~~~~~~~TkPP~ryTeasLi~~ME~~GIGtpATra~iI~~L~~R~Yv~~-~~k~l~pT~~G~~v~~~L~~~~~~l~~~~  538 (670)
T PRK05776        460 DVKVRKSYTKPPSRYSKASLLKWMESVGIGTEATRARIIETLFKRGYLTS-NGKYIEVTPLGFGVAEVLEKYFPDIVSVE  538 (670)
T ss_pred             eeeeeccccCCCCCCCHHHHHHHHhhCCCCCCccHHHHHHHHHhCCCEEe-eCCEEeECHHHHHHHHHHHHhccccCCHH
Confidence            99999999999999999999999999999999999999999999999997 67899999999999999988888999999


Q ss_pred             hHHHHHhhC
Q psy8714         554 MRSAYRVQA  562 (562)
Q Consensus       554 ~Ta~~E~~L  562 (562)
                      |||.||.+|
T Consensus       539 ~Ta~~E~~L  547 (670)
T PRK05776        539 LTRDFEEKL  547 (670)
T ss_pred             HHHHHHHHH
Confidence            999999876

>PRK14973 DNA topoisomerase I; Provisional

Probab=100.00  E-value=9.8e-130  Score=1117.15  Aligned_cols=532  Identities=31%  Similarity=0.514  Sum_probs=462.1

Q ss_pred             eEEEEecccCcCCcchHHhhcccccCCCCceeeeeee----eEcCCCcEEEEEEecccccccccccCCCCCccCC--CCC
Q psy8714           6 KKLVPASEIKLARPSLISLLTPLQRMNGACSVHEWVG----PLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVD--PLE   79 (562)
Q Consensus         6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~~~~~~~~~g----~~~g~~~~~~Vt~~~GHl~~l~~~~~y~~W~~~~--p~~   79 (562)
                      |+||||||     ||+|+.||+++|...... ..-+|    |++|+   ++||||.|||++|+|++.|++|+..+  |..
T Consensus         1 m~LiIAEK-----PSvAk~IA~~L~~~~~~~-~k~~g~~~~y~~~~---~~vt~~~GHLl~l~y~~~yk~W~~~~LPP~~   71 (936)
T PRK14973          1 MHLIIAEK-----NIAANRIAQILAGKTKVQ-VKKDGGVSTYSFDD---TVVVGLRGHVVEVDFEPGYTNWRSEEHTPRS   71 (936)
T ss_pred             CEEEEEcC-----HHHHHHHHHHhCCCCccc-cccCCCcceEEeCC---CEEEEEcccceecccCcccCCCccccCChhh
Confidence            57999999     999999999997542100 01133    55554   36999999999999999999998753  334


Q ss_pred             CCCCCcccccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHHH
Q psy8714          80 LFSCPTEKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAA  159 (562)
Q Consensus        80 ~~~~~~~~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~A  159 (562)
                      +++.+....  ....++++.|++++++||.||||||||||||+|||||+++++..   +.+++|+|+|||++|+++|++|
T Consensus        72 l~~~~~~~~--~~~kk~~~~Ik~l~k~ad~IiiAtD~DREGE~I~~~i~e~~~~~---~~~~~v~R~~fs~iT~~~I~~A  146 (936)
T PRK14973         72 LIDADTIKK--PTEKKIVGLIQKLAKKADRVTIATDFDTEGELIGKEAYELVRAV---NPKVPIDRARFSAITKEEIVTA  146 (936)
T ss_pred             ccCcceeec--CchHHHHHHHHHHHHhCCEEEECCCCCcchHHHHHHHHHHhhhc---cCCCceEEEEEccCCHHHHHHH
Confidence            554332111  22346888899999999999999999999999999999999743   3457999999999999999999


Q ss_pred             HHhCCCChHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhhhhhhhhhhcccCcceEEE
Q psy8714         160 MWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLL  239 (562)
Q Consensus       160 ~~nl~~~~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lIv~Re~eI~~F~p~~y~~i  239 (562)
                      |+||++++.++++||+||+++|||||||+||++|+.++..+    ++++|+||||||||+|||+||+||+||+|++||+|
T Consensus       147 ~~nl~~~d~~l~~A~~aR~~~D~lvG~nlSr~lt~~~~~g~----~~~lS~GRVQTPtL~lIveRe~EI~~Fvp~~Yw~I  222 (936)
T PRK14973        147 FAEPTDLDFALAAAGEARQIIDLIWGASLTRFISLAAHRGG----DNILSVGRVQSPTLAMIVDREKEIEAFVPEKYWML  222 (936)
T ss_pred             HhCCCCCcHHHHHHHHHHHHHHHHHHHHHhHHHHHHhhcCC----CcceeeccccchHHHHHHhHHHHHHcCCCCceEEE
Confidence            99999999999999999999999999999999999876321    34799999999999999999999999999999999


Q ss_pred             EEEEeeCCeEEEEEeecccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHHHHHHHHHhhCCCCHHHHHHH
Q psy8714         240 DLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQI  319 (562)
Q Consensus       240 ~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl~i  319 (562)
                      .+.+..+|..|.+.|..++|+|+++|+.+++.+.  .+++|++|++++++++||+||||++||++||+ |||||++||++
T Consensus       223 ~~~~~~~~~~~~a~~~~~r~~d~~~A~~i~~~~~--~~~~V~~v~~k~~~~~pP~Pf~ts~LQ~~ask-lg~Sa~kTm~i  299 (936)
T PRK14973        223 SLATEKDGEGIEARHTHGRFTDSAAAEAAYDATK--EPLVVTEVKEGHKVDRAPTPFDTTTFIVAASR-LGFSAANAMRI  299 (936)
T ss_pred             EEEEecCCceEEEEEcCCCCCCHHHHHHHHHHcC--CCeEEEEEEeeeEeccCCCCccHHHHHHHHHH-cCCCHHHHHHH
Confidence            9999877788999999999999999999999884  46899999999999999999999999999885 99999999999


Q ss_pred             HHHhHhcCceeecCCCCCCCCCcccHHHHHHHhccCCchhHHHHHHhhCCCCCCCCCCC-CCCCCCCccCCCcccCCCCH
Q psy8714         320 AERLYTQGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKD-VGDHPPITPTKLATRTQLDG  398 (562)
Q Consensus       320 aQ~LYE~glISYPRTds~~l~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~H~AI~PT~~~~~~~L~~  398 (562)
                      ||+|||+||||||||||++||+++++.+++..+... .|+..+..+..+....|+++++ ++|||||+||...+...|++
T Consensus       300 AQ~LYE~glITYPRTDS~~l~~~~~~~~il~~l~~~-~~~~~~~~l~~~~~~~~~~~kk~~~aH~AI~PT~~~~~~~Ls~  378 (936)
T PRK14973        300 AEDLYMNGYISYPRTDNTIYPKSLDLNGVLATLAKG-AFSKDVAWVKDNRRPVPTRGKKSSTDHPPIHPTGVATREELGD  378 (936)
T ss_pred             HHHHHhCCeeeccCcccccCchhhhHHHHHHHHHHh-hhHHHHHHHhhcCCccCCCCCCCcCCcCCccCcCCcChhhCCH
Confidence            999999999999999999999987777777766532 2444333222221122444444 68899999998766568999


Q ss_pred             HHHHHHHHHHHHHHhhcccCceEEEEEEEEEECCeEEEEEEEEEeecceeeeecccccccCCCCCCCCCCeeeeeeeEEe
Q psy8714         399 DAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKMV  478 (562)
Q Consensus       399 ~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~v~~~~~~~~~~Lp~l~~G~~~~~~~~~i~  478 (562)
                      +|++||+||||||||+||+||+|++|+|.++++++.|+++|++++++||+.||++++.++..||.+++||.+.+.++.+.
T Consensus       379 de~klY~LI~rRfLA~~~~~a~~~~t~v~~~~~~~~F~a~G~~i~~~Gw~~vy~~~~~~~~~LP~l~~Ge~~~~~~~~~~  458 (936)
T PRK14973        379 DRWKLYELVVRRFLATLSPDAEWATMKVNFDAGGEPYTATGGRLLEAGWRTVYPYSEAKENILPAFALGEKLPILAVNLE  458 (936)
T ss_pred             HHHHHHHHHHHHHHHHhChhheEEEEEEEEEECCEEEEEEEEEEeecCeeEeecccccccccCCCccCCCEEEeeeeEEe
Confidence            99999999999999999999999999999999999999999999999999999765444567999999999999999999


Q ss_pred             eeecCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEcCCCeeecchhHHHHHHhhhccCccCCChhhHHHH
Q psy8714         479 ERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAY  558 (562)
Q Consensus       479 e~~TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~~~k~l~~T~~G~~li~~l~~~~~~l~~p~~Ta~~  558 (562)
                      +++|+||+||||++||++||+.|||||||||+||++|++||||+   |+.|+||++|+.|+++|....+.|++|+|||.|
T Consensus       459 e~~T~PP~ryTEatLik~ME~~GIGTpATrA~II~~L~~R~Yve---~k~l~pT~~G~~li~~L~~~~~~l~~p~lTA~~  535 (936)
T PRK14973        459 EKETQPPARYSQSRLIQRMEELGLGTKSTRHEVIGKLVSRKYIE---GNPLRPTLVGRAVTESLEEHAGTITEPDMTQTL  535 (936)
T ss_pred             ecCCCCCCCCCHHHHHHHhccCCCCCcccHHHHHHHHHHccCee---CCceeEcHHHHHHHHHHHHhchhhcCHHHHHHH
Confidence            99999999999999999999999999999999999999999995   568999999999999998888899999999999


Q ss_pred             HhhC
Q psy8714         559 RVQA  562 (562)
Q Consensus       559 E~~L  562 (562)
                      |.+|
T Consensus       536 E~~L  539 (936)
T PRK14973        536 EEHM  539 (936)
T ss_pred             HHHH
Confidence            9876

>TIGR01057 topA_arch DNA topoisomerase I, archaeal

Probab=100.00  E-value=4.8e-129  Score=1085.63  Aligned_cols=531  Identities=24%  Similarity=0.380  Sum_probs=461.1

Q ss_pred             EecccCcCCcchHHhhcccccCCCCceeeeeee--eEc----CCCcEEEEEEecccccccccccC--CCCCccCCCCCCC
Q psy8714          10 PASEIKLARPSLISLLTPLQRMNGACSVHEWVG--PLF----GDLVLFKMTSVCGHIMGLDFTSK--YNNWDKVDPLELF   81 (562)
Q Consensus        10 ~ae~~~~~~p~~a~~~~~~~g~~~~~~~~~~~g--~~~----g~~~~~~Vt~~~GHl~~l~~~~~--y~~W~~~~p~~~~   81 (562)
                      ||||     ||+|+.||+++|.... +...-+|  ||+    |+  .|+||||.|||++|.+|++  |+.|+..+. +++
T Consensus         1 iAEK-----Ps~A~~ia~~l~~~~~-~~~~~~g~~y~~~~~~g~--~~~Vt~~~GHl~~l~~p~~~~~~~w~~~~l-P~~   71 (618)
T TIGR01057         1 IAEK-----PKVAAKIAGALSDGRV-LKKSEYGVPYWEVRRDGK--KIIVASAVGHLFGLHPKSRGGYPVFDIEWV-PIF   71 (618)
T ss_pred             CCCC-----hHHHHHHHHHhCCCCc-ccccCCCceEEEEecCCC--eEEEEEeccccccCCCccccCCCCCCcccC-cee
Confidence            6888     9999999999986521 0001245  665    54  5899999999999988764  666764321 222


Q ss_pred             CCCcccccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHHHHH
Q psy8714          82 SCPTEKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMW  161 (562)
Q Consensus        82 ~~~~~~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~A~~  161 (562)
                      +....+   ....++++.|++++++||+||||||||||||+|||+|+++++.      .+||+|+|||++|+++|++||+
T Consensus        72 ~~~~~~---~~~~~~~~~ik~l~~~~d~ii~AtD~DREGE~I~~~i~~~~~~------~~~v~Rl~~~~lt~~~I~~a~~  142 (618)
T TIGR01057        72 EFDKGK---GYVSKYIKALSKLAKGADEYINACDYDIEGEVIGFKALKYFCG------VERAKRMKFSTLTKQDIRRAYA  142 (618)
T ss_pred             eecCCc---ccHHHHHHHHHHHHhcCCEEEECCCCCccHHHHHHHHHHHhcc------CCCceEEEEccCCHHHHHHHHh
Confidence            211111   1113577888888899999999999999999999999999952      3789999999999999999999


Q ss_pred             hCCCChHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhhhhhhhhhhcccCcceEEEEE
Q psy8714         162 NLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDL  241 (562)
Q Consensus       162 nl~~~~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lIv~Re~eI~~F~p~~y~~i~~  241 (562)
                      ||++.+.+++.||.||+++|||||||+||++|+.++...|.  +.++|+||||||||+|||+||++|+||+|++||.|.+
T Consensus       143 nl~~~~~~l~~a~~aR~~~D~liG~n~Sr~~t~~~~~~~~~--~~~lS~GRVQtPtL~lvv~Re~eI~~F~p~~y~~i~~  220 (618)
T TIGR01057       143 NPEEIDYGMVDAGMARHILDWYWGINLSRALMEAIRAAAGR--WVILSAGRVQGPTLAFLVEREREINLFVPKPYWVIKA  220 (618)
T ss_pred             CcccCCHhHHHHHHHHHHHHHHHhhhhhHHHHHHhhccCCC--cccccccccchhHHHHHHHhHHHHHcCcCCccEEEEE
Confidence            99999999999999999999999999999999887643221  3479999999999999999999999999999999999


Q ss_pred             EEeeCCeEEEEEeecccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHHHHHHHHHhhCCCCHHHHHHHHH
Q psy8714         242 TLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAE  321 (562)
Q Consensus       242 ~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl~iaQ  321 (562)
                      .+..+++.|.+.|.+++++|+++|+++++.+++.+.++|+++++++++.+||+||||++||++||++|||||++||++||
T Consensus       221 ~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl~iaQ  300 (618)
T TIGR01057       221 TLEKGGGVFDARPEKWKIWSEEEAKSIKEELKKSPWAAVEEVRSERSILKPPPPFDLGTLQREAYRIFGFSPKKTQSIAQ  300 (618)
T ss_pred             EEecCCceEEEEEccCCcCCHHHHHHHHHHHhCCCCeEEEEEEeeeeeccCCCCccHHHHHHHHHHhcCCCHHHHHHHHH
Confidence            99888888999999899999999999999998754799999999999999999999999999999999999999999999


Q ss_pred             HhHhcCceeecCCCCCCCCCcccHHHHHHHhccCCchhHHHHHHhhCCCCCCCCCCCC-CCCCCCccCCCcccCCCCHHH
Q psy8714         322 RLYTQGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDV-GDHPPITPTKLATRTQLDGDA  400 (562)
Q Consensus       322 ~LYE~glISYPRTds~~l~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~H~AI~PT~~~~~~~L~~~e  400 (562)
                      +|||+||||||||||+|||+++++..+++.+...+.++.++..++.....+|++++++ +|||||+||...+...|+++|
T Consensus       301 ~LYe~g~ISYPRTds~~l~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~aH~aI~PT~~~~~~~L~~~e  380 (618)
T TIGR01057       301 ELYEEALISYPRTSSQKLPPSINYRAILDNLAKGPLYREAAERLLETGVLKPVEGKKEDPAHPAIHPTGEIPSQELSKDE  380 (618)
T ss_pred             HHHhcCceeecCcccCccCHHHhHHHHHHHHhcccchHHHHHHhhcccccccCCCCCCCCCCCCcCccCCCccccCCHHH
Confidence            9999999999999999999988777888888765566665554433233456666666 489999999765434799999


Q ss_pred             HHHHHHHHHHHHhhcccCceEEEEEEEEEECCeEEEEEEEEEeecceeeeecccccccCCCCCCCCCCeeeeeeeEEeee
Q psy8714         401 WRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKMVER  480 (562)
Q Consensus       401 ~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~v~~~~~~~~~~Lp~l~~G~~~~~~~~~i~e~  480 (562)
                      ++||+||+|||||+|||||+|++|+|.+.++++.|.++|++++++||+++|+.++.++..||.+++||.+.+.++.+.++
T Consensus       381 ~~iY~lI~~r~la~~~~~a~~~~t~v~~~~~~~~F~~~g~~~~~~Gw~~v~~~~~~~~~~lp~~~~gd~~~~~~~~~~e~  460 (618)
T TIGR01057       381 KKVYDLIVRRFLAAFSEEAIREKSKVLLRIGQEKFRLSGLRVVKLGWLEYYHYSKFEEKELPPLDRGDKIKVVRVDVRVK  460 (618)
T ss_pred             HHHHHHHHHHHHHHhChhhheeEEEEEEEECCeEEEEEEEEEEeCCcceeccCcccccccCCCCCCCCEeeeeeeeeccc
Confidence            99999999999999999999999999999999999999999999999999976544456699999999999999999999


Q ss_pred             ecCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEcCCCeeecchhHHHHHHhhhccCccCCChhhHHHHHh
Q psy8714         481 KTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRV  560 (562)
Q Consensus       481 ~TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~~~k~l~~T~~G~~li~~l~~~~~~l~~p~~Ta~~E~  560 (562)
                      +|+||+||||++||++||+.|||||||||+||++|++||||+. + ++|+||++|+.|+++|....+.|++|+|||.||.
T Consensus       461 ~TkPP~~~Te~tLi~~Me~~GIGTpATra~iIe~L~~r~Yi~~-~-~~l~pT~~G~~li~~l~~~~~~l~~p~~Ta~~E~  538 (618)
T TIGR01057       461 ETQPPARYDKASLIREMESRGLGTKATRARIIETLYKRGYIEG-K-KSIKVTPLGEAVIETLQRYCPEIISEELTRRFES  538 (618)
T ss_pred             ccCCCCCCCHHHHHHHHHhCCCCCCCcHHHHHHHHHhCCcEeE-C-CEEeeehHHHHHHHHHHHhchhhcChhhHHHHHH
Confidence            9999999999999999999999999999999999999999986 4 4799999999999999877778999999999998


Q ss_pred             hC
Q psy8714         561 QA  562 (562)
Q Consensus       561 ~L  562 (562)
                      +|
T Consensus       539 ~L  540 (618)
T TIGR01057       539 KL  540 (618)
T ss_pred             HH
Confidence            76

This model describes topoisomerase I from archaea. These enzymes are involved in the control of DNA topology. DNA topoisomerase I belongs to the type I topoisomerases, which are ATP-independent.

>PRK07219 DNA topoisomerase I; Validated

Probab=100.00  E-value=3.8e-129  Score=1114.57  Aligned_cols=540  Identities=30%  Similarity=0.523  Sum_probs=467.8

Q ss_pred             eEEEEecccCcCCcchHHhhcccccCCCCceeeeeee--eEc--CCCcEEEEEEecccccccccccCCCCCccCCCCCCC
Q psy8714           6 KKLVPASEIKLARPSLISLLTPLQRMNGACSVHEWVG--PLF--GDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELF   81 (562)
Q Consensus         6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~~~~~~~~~g--~~~--g~~~~~~Vt~~~GHl~~l~~~~~y~~W~~~~p~~~~   81 (562)
                      |.||||||     ||+|+.||+++|..+. +...-+|  ||+  +++..|+|+|+.|||++|++|++|+.|+..+|..++
T Consensus         1 ~~LiIaEK-----ps~Ak~Ia~~L~~g~~-~~~~~~g~~~~~~~~~g~~~~v~~~~GHl~~l~~p~~y~~w~~~~l~~l~   74 (822)
T PRK07219          1 TELIIAEK-----NNAARRIADILSGGKA-KKKRVNGVPYYEFERKGEKWIVIGLSGHIVTVDFPEEYGDWRDVDPAELI   74 (822)
T ss_pred             CEEEEEeC-----HHHHHHHHHHhcCCCc-ccccCCCcceEEecCCCCeEEEEEecCcccccCCchhcCCcCcCChhhcc
Confidence            58999999     9999999999942211 0001123  444  222358999999999999999999999877654444


Q ss_pred             CCCcccccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHHHHH
Q psy8714          82 SCPTEKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMW  161 (562)
Q Consensus        82 ~~~~~~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~A~~  161 (562)
                      ..+...  ...+.++++.|++++++||+||||||||||||+|||+|++.+...    ++++|+|+|||++|+++|++||+
T Consensus        75 ~~~~~~--~~~~~~~~~~lk~l~~~ad~iiiAtD~DREGE~I~~ei~~i~~~~----~~~~v~R~~fs~iT~~~I~~A~~  148 (822)
T PRK07219         75 DADPVK--KITKQNYINALKKLAKDADEIIIATDYDREGELIGKEAYHILREV----CQVPVKRARFSSLTKKEIRKAFE  148 (822)
T ss_pred             ccceee--cCCHHHHHHHHHHHHhcCCEEEEcCCCChhHHHHHHHHHHHHHhc----CCCceeEEEEccCCHHHHHHHHh
Confidence            322111  122446888999999999999999999999999997777666432    25899999999999999999999


Q ss_pred             hCCCChHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhhhhhhhhhhcccCcceEEEEE
Q psy8714         162 NLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDL  241 (562)
Q Consensus       162 nl~~~~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lIv~Re~eI~~F~p~~y~~i~~  241 (562)
                      ||+++|.++++||+|||++|||||||+||++|+.+++. |.  ..++|+||||||||+|||+||+||+||+|++||+|.+
T Consensus       149 n~~~~d~~l~~a~~aR~~~D~lvG~nlSr~lt~~~~~~-g~--~~~lS~GRVQtPtL~lIv~Re~eI~~F~p~~yw~i~~  225 (822)
T PRK07219        149 NPDEIDFNLADAGEARQIIDLYWGAALTRFLSLSVRQL-GR--WDFLSVGRVQTPTLAFIVDREREIRAFDPEDYWKIEA  225 (822)
T ss_pred             CcccCCHHHHHHHHHHHHHHHHhhhhhCHHHHHHHHhc-cc--cCccccccccchhhHHHHHHHHHHHcCCCcccEEEEE
Confidence            99999999999999999999999999999999987643 21  2479999999999999999999999999999999999


Q ss_pred             EEeeCCeEEEEEe----ecccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHHHHHHHHHhhCCCCHHHHH
Q psy8714         242 TLNLNGVAVSVTW----SRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAM  317 (562)
Q Consensus       242 ~~~~~~~~~~~~~----~~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl  317 (562)
                      .+..++..|.+.|    ..++++|+++|+++++.+.+.+.++|.+|++++++.+||+||||++||++||++|||||++||
T Consensus       226 ~~~~~~~~~~~~~~~~~~~~r~~d~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~t~~Lq~~a~~~~g~sa~~tm  305 (822)
T PRK07219        226 LLDKEAQYFYRDLIGGHEAEKFWDEEEAEEIYEKLKGAKEATVSSVKKRERTISPPAPFNTTEFLREASKIFGISPKRAM  305 (822)
T ss_pred             EEEecCcceeeecccccccCccCCHHHHHHHHHHhcCCCCeEEEEEEEeeEEccCCCCccHHHHHHHHHHHcCCCHHHHH
Confidence            9976555566655    456899999999999999864579999999999999999999999999999999999999999


Q ss_pred             HHHHHhHhcCceeecCCCCCCCCCcccHHHHHHHhccCCchhHHHHHHhhCCCCCCCCCCC-CCCCCCCccCCCcccCCC
Q psy8714         318 QIAERLYTQGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKD-VGDHPPITPTKLATRTQL  396 (562)
Q Consensus       318 ~iaQ~LYE~glISYPRTds~~l~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~H~AI~PT~~~~~~~L  396 (562)
                      ++||+|||+||||||||||++||+++++.++++.+.....|+.++..++.....+|+++++ ++||||||||...+.+.|
T Consensus       306 ~iaQ~LYe~glITYpRTds~~l~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~~~~~~~~~~~~~aH~aI~PT~~~~~~~L  385 (822)
T PRK07219        306 EIAEKLYTAGYISYPRTDNTVYPDDLDPKELLKKLSKKKEYGPYAESILEQENIKPTEGKKETTDHPPIHPVDVPKREEL  385 (822)
T ss_pred             HHHHHHHhCCceeccCcccccCCHHHHHHHHHHHhhcccchhhHhhhhcccCCcccCCCCCCCCCCCCCCCcCCCCcccC
Confidence            9999999999999999999999998877788888876666777665555433345666554 689999999997654689


Q ss_pred             CHHHHHHHHHHHHHHHhhcccCceEEEEEEEEEECCeEEEEEEEEEeecceeeeecccccccCCCCCCCCCCeeeeeeeE
Q psy8714         397 DGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVK  476 (562)
Q Consensus       397 ~~~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~v~~~~~~~~~~Lp~l~~G~~~~~~~~~  476 (562)
                      +++|++||+||+|||||+||+||+|++|+|.++++++.|+++|++++++||+++|+++..++..||.|++||.+.+.++.
T Consensus       386 ~~~e~~lY~LI~rrfla~~~~~a~~~~t~v~~~~~~~~F~a~g~~i~~~Gw~~vy~~~~~~~~~lP~l~~G~~~~~~~~~  465 (822)
T PRK07219        386 SDDEWKVYELIVRRFLATLADPAEWEYLKVELDVNGEIFKASGSRLVEEGWHEVYPYEKFDEKELPDLEEGEKLKVNKIE  465 (822)
T ss_pred             CHHHHHHHHHHHHHHHHHhCccceeeEEEEEEEeCCeEEEEEEEEEccCCcHhhcCccccccccCCCCCCCCEeeeeeeE
Confidence            99999999999999999999999999999999999999999999999999999997665445679999999999999999


Q ss_pred             EeeeecCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEcCCCeeecchhHHHHHHhhhccCccCCChhhHH
Q psy8714         477 MVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRS  556 (562)
Q Consensus       477 i~e~~TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~~~k~l~~T~~G~~li~~l~~~~~~l~~p~~Ta  556 (562)
                      +.+++|+||+||||++||++||+.|||||||||+||++|++|||| + +|+.|+||++|+.|+++|....+.|++|+|||
T Consensus       466 ~~~~~T~PP~rytea~Li~~Me~~GIGT~ATra~iI~~L~~R~Yv-~-~~~~l~pT~~G~~l~~~l~~~~~~l~~~~~Ta  543 (822)
T PRK07219        466 IEAKETQPPKRYTQSSLIKEMEKRGLGTKATRHDIIEKLYKRGYV-I-EGDPPRPTDLGIAVIEALEKYAPEIVSEEMTA  543 (822)
T ss_pred             ecccccCCCCCCCHHHHHHHHHhCCCCCCccHHHHHHHHHhcCcE-e-cCCEeeecHHHHHHHHHHHHhchhhcChhHHH
Confidence            999999999999999999999999999999999999999999999 6 57799999999999999988888999999999


Q ss_pred             HHHhhC
Q psy8714         557 AYRVQA  562 (562)
Q Consensus       557 ~~E~~L  562 (562)
                      .||..|
T Consensus       544 ~~E~~L  549 (822)
T PRK07219        544 QLEADM  549 (822)
T ss_pred             HHHHHH
Confidence            999876

>PRK14724 DNA topoisomerase III; Provisional

Probab=100.00  E-value=1.8e-128  Score=1116.69  Aligned_cols=540  Identities=24%  Similarity=0.343  Sum_probs=447.0

Q ss_pred             eEEEEecccCcCCcchHHhhcccccCCCCceeeeeeeeEcCCCcEEEEEEecccccccccccCC----CCCccCCCCCCC
Q psy8714           6 KKLVPASEIKLARPSLISLLTPLQRMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKY----NNWDKVDPLELF   81 (562)
Q Consensus         6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~~~~~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~~~~y----~~W~~~~p~~~~   81 (562)
                      |+||||||     ||+|+.||.++|-+.... ...+|||+|++  |+||||+|||++|..|++|    ++|+..++. ++
T Consensus         2 k~LiIAEK-----PSvAk~IA~aL~~~~g~~-~k~~gy~eg~~--~~Vtwa~GHL~eL~~Pe~y~~~~~~W~~~~LP-ii   72 (987)
T PRK14724          2 KTLVIAEK-----PSVAQDIVRALTPVAGKF-EKHDEHFESDS--YVVTSAVGHLVEIQAPEEFDVKRGKWSFANLP-VI   72 (987)
T ss_pred             CEEEEEeC-----HHHHHHHHHHhhhccCCC-cCCCceecCCC--EEEEecccccccCCChhhcccccCCccccccc-cC
Confidence            57999999     999999999994211111 12478999874  8999999999999876665    568765421 22


Q ss_pred             CCCcccccCCCCCchHHHHHhhc--ccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHHH
Q psy8714          82 SCPTEKREATPKLKLPAFLANEA--KDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAA  159 (562)
Q Consensus        82 ~~~~~~~~~~~~~~~i~~L~~~~--~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~A  159 (562)
                      +.+..........++++.|++++  +++|+||||||||||||+|||+|+++++... .+.++||+|+||||||+++|++|
T Consensus        73 P~~f~~~~~~~~k~q~~~Ik~l~k~~~~~~II~AtD~DREGElI~~~I~~~~~~~~-~~~~kpv~Rlw~sslT~~aI~~a  151 (987)
T PRK14724         73 PPYFDLKPVDKTKTRLNAVVKLAKRKDVTELVNACDAGREGELIFRLIEQYAGGAK-GGLGKPVKRLWLQSMTPQAIRDG  151 (987)
T ss_pred             CccceeeeccchHHHHHHHHHHHhhCCCCeEEECCCCCcchhHHHHHHHHHhCccc-ccCCCceEEEEEccCCHHHHHHH
Confidence            21111000111123444444444  5788999999999999999999999995210 01148999999999999999999


Q ss_pred             HHhCCCChH--hHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhhhhhhhhhhcccCcceE
Q psy8714         160 MWNLVKPNI--FEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYW  237 (562)
Q Consensus       160 ~~nl~~~~~--~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lIv~Re~eI~~F~p~~y~  237 (562)
                      |+||++++.  ++++||.||+++|||||||+||++|+..+...+   ..++|+||||||||+|||+||+||+||+|++||
T Consensus       152 f~nlr~~~~~~~L~~Aa~aR~~aDwLvG~N~SR~~T~~~~~~~~---~~~lSvGRVQTPtL~lVv~Re~eI~~F~p~~Y~  228 (987)
T PRK14724        152 FDNLRSDAQMQGLASAARSRSEADWLVGINGTRAMTAFNSRDGG---FFLTTVGRVQTPTLSLVVEREEKIRKFVSRDYW  228 (987)
T ss_pred             HhCCCCchhhhhHHHHHHHHHHHHHHhHHHHhHHHHHHHHhcCC---cceeccccchhHHHHHHHHHHHHHHhCCCCccE
Confidence            999999884  899999999999999999999999985432211   126899999999999999999999999999999


Q ss_pred             EEEEEEeeCCeEEEEEee--------------cccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHHHHHH
Q psy8714         238 LLDLTLNLNGVAVSVTWS--------------RGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMR  303 (562)
Q Consensus       238 ~i~~~~~~~~~~~~~~~~--------------~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~  303 (562)
                      +|.+.|..+++.|.+.|.              .++++++++|+++++.|.+ +.++|.+ +.+++++.||+||||++||+
T Consensus       229 ~i~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~A~~i~~~~~~-~~~~V~~-~~k~~~~~pP~pf~Lt~LQ~  306 (987)
T PRK14724        229 EIHAGFHAEAGEYLGKWFDPQWKKASDDPEARADRVWSEREARAIADAVRG-KAATVTE-ESKPTTQASPLLFDLTSLQR  306 (987)
T ss_pred             EEEEEEecCCCceeEEEeecccccccccccccccccCCHHHHHHHHHHhcC-CCeEEEE-eeeeEecCCCCCCcHHHHHH
Confidence            999999877777888772              2579999999999999986 4789988 89999999999999999999


Q ss_pred             HHHhhCCCCHHHHHHHHHHhHhc-CceeecCCCCCCCCCcc--cHHHHHHHhccC--CchhHHHHHHhhCCC--CCCCC-
Q psy8714         304 VASSGLGMGPHHAMQIAERLYTQ-GYVSYPRTETTQYPENF--DLVAVLRQQESS--PDWGDHVREVLSNGI--SKPRK-  375 (562)
Q Consensus       304 ~a~~~~g~s~~~tl~iaQ~LYE~-glISYPRTds~~l~~~~--~~~~~l~~l~~~--~~~~~~~~~~~~~~~--~~~~~-  375 (562)
                      +||++|||||++||++||+|||+ ||||||||||+|||+++  .+..+|+.|...  +.+..++...+....  ...+. 
T Consensus       307 eA~~~~g~Sa~~TL~iAQ~LYE~~klITYPRTDS~~l~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~~~~~~~~~~r~~  386 (987)
T PRK14724        307 EANGKFGFSAKTTLALAQSLYERHKALTYPRTDSRALPEDYLPVAKQTFEMLATSGMRHLAPFAQQALDGNYVRPSKRIF  386 (987)
T ss_pred             HHHHHcCCCHHHHHHHHHHHHHcCCeEeecCcCCccCCHHHHHHHHHHHHHHhcccchhHHHHHHHHhcccccCCCCCcC
Confidence            99999999999999999999996 99999999999999986  477788777543  334444433333211  12222 


Q ss_pred             -CCCCCCCCCCccCCCcccCCCCHHHHHHHHHHHHHHHhhcccCceEEEEEEEEEECCeEEEEEEEEEeecceeeeeccc
Q psy8714         376 -GKDVGDHPPITPTKLATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWS  454 (562)
Q Consensus       376 -~~~~~~H~AI~PT~~~~~~~L~~~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~v~~~~  454 (562)
                       .++++||||||||...+ ..|+++|++||+||+|||||+|||||+|++|+|.+.++++.|+++|++++++||+.||+.+
T Consensus       387 ~~~Kv~~H~AIiPT~~~p-~~Ls~~E~kiY~lI~rRfla~f~~~a~~~~t~v~~~~~~~~F~a~G~~i~~~GW~~vy~~~  465 (987)
T PRK14724        387 DNSKVSDHFAIIPTTQAP-SGLSEAEQKLYDLVVRRFMAVFFPSAEYQVTTRISQVVGHSFKTEGKVLVKPGWLAIYGKE  465 (987)
T ss_pred             CCCCCCCcCCcCCCCCCc-ccCCHHHHHHHHHHHHHHHHHhCchhEEEEEEEEEEecCcEEEEEEEEECcCChHHHhCcc
Confidence             34568999999998765 6899999999999999999999999999999999999999999999999999999998643


Q ss_pred             cc----------ccCCCCCCCCCCeeeeeeeEEeeeecCCCCCCCHHHHHHHHH----------------hcCCCCcCch
Q psy8714         455 AM----------KNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLME----------------KHGIGTDASI  508 (562)
Q Consensus       455 ~~----------~~~~Lp~l~~G~~~~~~~~~i~e~~TkPP~~~Te~~Li~~Me----------------~~GIGTpATr  508 (562)
                      ..          ++..||.|++||.+.+.++.+.+++|+||+||||++||++||                +.||||||||
T Consensus       466 ~~~~~~~~~~~~~~~~LP~l~~Ge~v~~~~~~~~e~~TkPP~ryTEatLl~aME~~gk~v~d~el~~~~~~~GIGTpATR  545 (987)
T PRK14724        466 AANEVEDAKDGDKGQPLVPVKPGEMVRTEFAEAKGLKTKPPARYSEATLLGAMESAGKQIDDDELREAMQEKGLGTPATR  545 (987)
T ss_pred             ccccccccccccccccCCCcCCCCEeeeeeccccccccCCCCCcCHHHHHHHHHhhhhcccchhhhhhhhcCCCCCcccH
Confidence            21          123599999999999999999999999999999999999998                5799999999


Q ss_pred             hHHHHHhhcCCeEEEcCCCeeecchhHHHHHHhhhcc-CccCCChhhHHHHHhhC
Q psy8714         509 PVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKI-DRELVEPTMRSAYRVQA  562 (562)
Q Consensus       509 a~iI~~L~~r~Yi~~~~~k~l~~T~~G~~li~~l~~~-~~~l~~p~~Ta~~E~~L  562 (562)
                      |+||++|++||||++ +|+.|+||++|+.||++|... +++|++|+|||.||.+|
T Consensus       546 A~IIe~L~~r~Yi~~-~~k~l~pT~~G~~li~~L~~~~~~~l~~pelTa~wE~~L  599 (987)
T PRK14724        546 AAIIEGLLTEKYMLR-EGRELIPTAKAFQLMTLLRGLGVEELSRAELTGEWEYKL  599 (987)
T ss_pred             HHHHHHHHhCCcEEe-cCCEEeEcHHHHHHHHHHHhcCchhhcChhHHHHHHHHH
Confidence            999999999999997 678999999999999998654 56799999999999976

>COG0550 TopA Topoisomerase IA [DNA replication, recombination, and repair]

Probab=100.00  E-value=4e-128  Score=1053.48  Aligned_cols=511  Identities=30%  Similarity=0.451  Sum_probs=443.7

Q ss_pred             eEEEEecccCcCCcchHHhhcccccCCCCceeeeeeeeEcCCCcEEEEEEecccccccccccCCCCCccCCCCCCCCCCc
Q psy8714           6 KKLVPASEIKLARPSLISLLTPLQRMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPT   85 (562)
Q Consensus         6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~~~~~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~~~~y~~W~~~~p~~~~~~~~   85 (562)
                      |.||||||     |+.|+.|++.+|.+                  |+|+||+|||++|..|++++.|...+...+.+...
T Consensus         1 ~~LiIvEs-----PskAk~Ia~~Lg~~------------------~~V~as~GHi~dl~~~~~~~~~~~~~~~~~~~~~~   57 (570)
T COG0550           1 KRLIIVES-----PSKAKTIAKYLGKG------------------YVVTASVGHLRDLPFPEEYKGWVDVDLPIFEPKYI   57 (570)
T ss_pred             CeEEEEeC-----HHHHHHHHHhcCCC------------------cEEEEcccccccCCChhhccCCcCCccccccccee
Confidence            68999999     99999999655543                  68999999999999988888898755332222111


Q ss_pred             ccccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHHHHHhCCC
Q psy8714          86 EKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNLVK  165 (562)
Q Consensus        86 ~~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~A~~nl~~  165 (562)
                      .....  +.++++.|+.++++||.||||||||||||+|||||+++++..   + ..+++|+|||+||+++|++||+|+++
T Consensus        58 ~~~~~--k~~~v~~lk~~ak~ad~v~lAtD~DREGE~I~~~i~~~l~~~---~-~~~~~R~~F~eiT~~aI~~A~~~p~~  131 (570)
T COG0550          58 IKPGK--KKKVVKKLKKLAKKADEVYLATDPDREGEAIGWHILEVLKLK---N-PSKVKRVVFSEITKKAILSAFKNPRE  131 (570)
T ss_pred             ccchh--hHHHHHHHHHHhccCCEEEECCCCCcchHHHHHHHHHHhCcc---C-CCceeEEEEecCCHHHHHHHHhCchh
Confidence            11110  446888999999999999999999999999999999999642   1 14699999999999999999999999


Q ss_pred             ChHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhhhhhhhhhhcccCcceEEEEEEEee
Q psy8714         166 PNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNL  245 (562)
Q Consensus       166 ~~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lIv~Re~eI~~F~p~~y~~i~~~~~~  245 (562)
                      .|+++++||+||+++|||+|+|+||++|+.+++       +++|+||||||||+|||+||+||++|+|++||+|.+.+..
T Consensus       132 id~~lv~A~~aR~~lD~lvG~~lSr~l~~~~~~-------~~LSaGRVQSpaL~lVveRE~EI~~F~p~~yw~i~a~~~~  204 (570)
T COG0550         132 IDMNLVDAQLARRILDRLVGYNLSRLLWKKLKR-------GVLSAGRVQSPALRLVVEREREIEAFVPEEYWEIKAIFEK  204 (570)
T ss_pred             hchHHHHHHHHHHHHHHHhhhhhhHHHHHhhcc-------CCCCCccccchhhhhhHhhHHHHHhCCCCcceEEEEEEec
Confidence            999999999999999999999999999987653       1599999999999999999999999999999999999988


Q ss_pred             CCeEEEEEee------cccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHHHHHHHHHhhCCCCHHHHHHH
Q psy8714         246 NGVAVSVTWS------RGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQI  319 (562)
Q Consensus       246 ~~~~~~~~~~------~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl~i  319 (562)
                      +++.|.+.|.      .+++.+...|.++++.+++ +.+.|.+++.++++..||+||+|++||++||++|||||++||++
T Consensus       205 ~~~~f~a~~~~~~~~~~~~~~~~~~a~~~~~~l~~-~~~~V~~ve~k~~~~~pp~Pf~tstLQq~As~~lgfs~kktm~i  283 (570)
T COG0550         205 GGGEFSARLTEIEGKKEGRLKDKDEAEEIVNKLKG-KPAKVVSVEKKPKKRSPPPPFTTSTLQQEASRKLGFSAKKTMDI  283 (570)
T ss_pred             CCccEEEEEeccccccccccccHHHHHHHHHHccC-CceEEEEEeeeeeccCCCCCCcHHHHHHHHHHhCCCCHHHHHHH
Confidence            7766998886      3467888999999999985 57999999999999999999999999999999999999999999


Q ss_pred             HHHhHhc-CceeecCCCCCCCCCccc--HHHHHHHhccCCchhHHHHHHhhC-CCCCCCCCC-CCCCCCCCccCC-Cccc
Q psy8714         320 AERLYTQ-GYVSYPRTETTQYPENFD--LVAVLRQQESSPDWGDHVREVLSN-GISKPRKGK-DVGDHPPITPTK-LATR  393 (562)
Q Consensus       320 aQ~LYE~-glISYPRTds~~l~~~~~--~~~~l~~l~~~~~~~~~~~~~~~~-~~~~~~~~~-~~~~H~AI~PT~-~~~~  393 (562)
                      ||+|||. ||||||||||++||+++.  ....+....    |+.   .++.. ....+.+++ +.+||||||||+ ..+ 
T Consensus       284 AQ~LYE~~glITYpRTDs~~ls~~~~~~~~~~i~~~~----yg~---~~l~~~~~~~~~~~~~~q~AHeAIrPT~~~~p-  355 (570)
T COG0550         284 AQKLYEGHGLITYPRTDSTRLSEEALAEARLYILAIA----YGK---EYLPLKPRRYPSKGKKAQEAHEAIRPTDFETP-  355 (570)
T ss_pred             HHHHhcCCCcEEecCCCCCcCCHHHHHHHHHHHHhhc----cHH---hhcccccccCCCCCCCCcCCCCCcCCCCCCCc-
Confidence            9999997 999999999999999863  233333221    433   34432 122333433 348899999997 322 


Q ss_pred             CCCC-HHHHHHHHHHHHHHHhhcccCceEEEEEEEEEECCeEEEEEEEEEeecceeeeeccc--ccccCCCCCCCCCCee
Q psy8714         394 TQLD-GDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWS--AMKNESIPDFKPGDLI  470 (562)
Q Consensus       394 ~~L~-~~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~v~~~~--~~~~~~Lp~l~~G~~~  470 (562)
                      ..+. .||++||+|||||||||||+||+|++++|++.++++.|+++|++++++||+.||++.  +.++..||.+++||.+
T Consensus       356 ~~~~~~de~klY~LI~rrflAs~m~~A~~~~~~v~l~~~~~~F~a~g~~~~~~Gw~~vy~~~~~~~~~~~lP~l~~gd~l  435 (570)
T COG0550         356 ESLKAYDELKLYDLIWRRFLASQMPDAIYEKTTVTLEVAGEKFKASGKVLKFDGWLKVYGEDKDEEEDKELPELKEGDEL  435 (570)
T ss_pred             ccccchhHHHHHHHHHHHHHHHhCchhhheEEEEEEEecCcEEEEeeeEEecCcHHHhhcccccccccccCCCCCCCCee
Confidence            2333 799999999999999999999999999999999999999999999999999999865  2226789999999999


Q ss_pred             eeeeeEEeeeecCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEcCCCeeecchhHHHHHHhhhccCccCC
Q psy8714         471 PIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELV  550 (562)
Q Consensus       471 ~~~~~~i~e~~TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~~~k~l~~T~~G~~li~~l~~~~~~l~  550 (562)
                      .+.++++.+++|+||+||||++||++||+.|||||||||+||++|++||||.. +|+.|+||++|+.|++.|...++.++
T Consensus       436 ~~~~~~~~~~~T~PP~rytEasLvk~mE~~GIGrpSTyA~iI~~L~~RgYv~~-~~~~~~pT~~G~~v~~~L~~~f~~l~  514 (570)
T COG0550         436 KVEKLEVEEHFTKPPPRYTEASLVKAMEKLGIGTPSTYASIIETLQKRGYVEK-KGKRLVPTELGEAVIELLEEYFPELV  514 (570)
T ss_pred             EEeeeeecccccCCcCCCCHHHHHHHHHhCCCCCcccHHHHHHHHhcCCcEEe-cCCeeEEcHHHHHHHHHHHHhchhhc
Confidence            99999999999999999999999999999999999999999999999999998 67899999999999999999999999


Q ss_pred             ChhhHHHHHhhC
Q psy8714         551 EPTMRSAYRVQA  562 (562)
Q Consensus       551 ~p~~Ta~~E~~L  562 (562)
                      +|+|||.||+.|
T Consensus       515 ~~~~Ta~mE~~L  526 (570)
T COG0550         515 DPDFTAKMEEKL  526 (570)
T ss_pred             CHHHHHHHHHHH
Confidence            999999999986

>TIGR01056 topB DNA topoisomerase III, bacteria and conjugative plasmid

Probab=100.00  E-value=2e-127  Score=1074.32  Aligned_cols=530  Identities=23%  Similarity=0.334  Sum_probs=448.4

Q ss_pred             eEEEEecccCcCCcchHHhhcccccCCCCceeeeeeeeEc-CCCcEEEEEEecccccccccc----cCCCCCccCCCCCC
Q psy8714           6 KKLVPASEIKLARPSLISLLTPLQRMNGACSVHEWVGPLF-GDLVLFKMTSVCGHIMGLDFT----SKYNNWDKVDPLEL   80 (562)
Q Consensus         6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~~~~~~~~~g~~~-g~~~~~~Vt~~~GHl~~l~~~----~~y~~W~~~~p~~~   80 (562)
                      |+||||||     ||+|+.|++++|..+.     -+|||+ |.+  |+|+||+|||++|..|    ++|++|+..++ ++
T Consensus         1 ~~LiIaEK-----Ps~Ak~Ia~~L~~~~~-----~~gy~e~g~~--~~V~~~~GHl~~L~~p~~~~~~~~~W~~~~l-p~   67 (660)
T TIGR01056         1 MTLVLCEK-----PSQARDLATVLAKKKK-----GNGYLEIGVG--GFVTWAVGHLVELAEPEEYDEKYKNWRTYDL-PL   67 (660)
T ss_pred             CeEEEEeC-----HHHHHHHHHHhCCCcC-----CCCcEEECCc--EEEEeCchhhhcCCChhhcccccCccccCCC-Cc
Confidence            68999999     9999999999986642     488999 874  7899999999999755    45668876442 11


Q ss_pred             CCCCcccccCCCCCchHHHHHhhcc--cCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHH
Q psy8714          81 FSCPTEKREATPKLKLPAFLANEAK--DCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKA  158 (562)
Q Consensus        81 ~~~~~~~~~~~~~~~~i~~L~~~~~--~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~  158 (562)
                      .+..........+.++++.|+++++  +||+||||||||||||+|||||+++++.    +...+|+|+|||++|+++|++
T Consensus        68 ~p~~f~~~~~~~~~~~~~~ik~l~k~~~ad~Ii~AtDpDREGE~I~~~i~~~l~~----~~~~~v~Ri~f~~iT~~~I~~  143 (660)
T TIGR01056        68 EPEDWQLVVSDKTKKQFNVIKRILKENKVDEVVIATDPDREGELIAREILDYLKV----TDKVTIKRLWISSLVDSSIRK  143 (660)
T ss_pred             ccccceeeeccchHHHHHHHHHHhhhcCCCEEEECCCCCcchHHHHHHHHHHhCC----CCCCceEEEEeccCCHHHHHH
Confidence            1111000111223467888888888  9999999999999999999999999952    112399999999999999999


Q ss_pred             HHHhCCCC--hHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhhhhhhhhhhcccCcce
Q psy8714         159 AMWNLVKP--NIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPY  236 (562)
Q Consensus       159 A~~nl~~~--~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lIv~Re~eI~~F~p~~y  236 (562)
                      ||+||+++  +.++++||.||+++|||||||+||++|+.++..+.   +..+|+||||||||+|||+||+||+||+|++|
T Consensus       144 A~~n~~~~~~~~~l~~a~~aR~~~D~lvG~nlSr~lt~~~~~~g~---~~~lS~GRVQtptL~lIveRe~eI~~F~p~~y  220 (660)
T TIGR01056       144 AFKNLRPKSETEGLYKSGVARARADWLVGINLTRAFTKLGREAGN---DGVLSVGRVQTPTLAMVVKRENEIKNFVGKPF  220 (660)
T ss_pred             HHHcCCCchhhhhHHHHHHHHHHHHHHHHHhHhHHHHHhhhhcCC---CCceecccchhhhhHHHHHHHHHHHcCCCCcc
Confidence            99999986  67899999999999999999999999987654311   24699999999999999999999999999999


Q ss_pred             EEEEEEEeeCCeEEEEEeec-----ccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHHHHHHHHHhhCCC
Q psy8714         237 WLLDLTLNLNGVAVSVTWSR-----GHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGM  311 (562)
Q Consensus       237 ~~i~~~~~~~~~~~~~~~~~-----~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~  311 (562)
                      |+|.+.+..++..|.+.|..     .+++|+++|+.+++.+.+ .+++|.+|+.++++.+||+||||++||++||++|||
T Consensus       221 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~i~~~~~~-~~~~V~~v~~k~~~~~pP~pf~ts~LQ~~as~~~g~  299 (660)
T TIGR01056       221 YEVSATINKDEQEFTTEWQPYKDEEERELHEFLAENVVTDLTQ-KPALVTDIEKERKKTSAPLFYDLSALQEDANKRFGI  299 (660)
T ss_pred             EEEEEEEEcCCceEEEEEeccCCcccCcCCHHHHHHHHHHhhC-CCeEEEEEEeeeeecCCCCCCCHHHHHHHHHHhcCC
Confidence            99999998777789999853     579999999999999976 468999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHhHhc-CceeecCCCCCCCCCcc--cHHHHHHHhccCCchhHHHHHHhhCCCCCCC--CCCCCCCCCCCc
Q psy8714         312 GPHHAMQIAERLYTQ-GYVSYPRTETTQYPENF--DLVAVLRQQESSPDWGDHVREVLSNGISKPR--KGKDVGDHPPIT  386 (562)
Q Consensus       312 s~~~tl~iaQ~LYE~-glISYPRTds~~l~~~~--~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~H~AI~  386 (562)
                      ||++||++||+|||+ ||||||||||++||+++  ++.++|+.+.... +......... ...+.+  +.++++||||||
T Consensus       300 s~~~tm~iAQ~LYE~~glITYpRTDS~~ls~~~~~~~~~~i~~~~~~~-~~~~~~~~~~-~~~~~~~~~~~~~~aH~AI~  377 (660)
T TIGR01056       300 SAKRTLDIAQKLYETHKLITYPRTDSRYLPEDEKEMLLEVLDALKVIT-PALLPIKKRD-ELTNNRLWNDKKIEDHHAII  377 (660)
T ss_pred             CHHHHHHHHHHHHHhCCEEEEecCCCccCCHHHHHHHHHHHHHhhccc-hhhhcccccc-cccccCcCCCCccCCcCCcc
Confidence            999999999999998 99999999999999986  4666776654321 1111100001 001111  223457899999


Q ss_pred             cCCCcc-cCCCCHHHHHHHHHHHHHHHhhcccCceEEEEEEEEEECCeEEEEEEEEEeecceeeeecccccc----cCCC
Q psy8714         387 PTKLAT-RTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMK----NESI  461 (562)
Q Consensus       387 PT~~~~-~~~L~~~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~v~~~~~~~----~~~L  461 (562)
                      ||...+ ...|+++|++||+||++||||+||+||+|++|+|.+.++++.|+++|++++++||+.+|+..+.+    +..|
T Consensus       378 PT~~~~~~~~L~~de~klY~LI~~Rflas~~~~a~~~~t~v~~~~~~~~F~a~g~~i~~~Gw~~v~~~~~~~~~~~~~~L  457 (660)
T TIGR01056       378 PTGNDFNLSDLSEEERNVYKLIAQNYLMQFMPKEEYETTTIEIAIGKLMFEAKGKILQDNGWKALLGKQEEDEETEDTTL  457 (660)
T ss_pred             ccCCccccccCCHHHHHHHHHHHHHHHHHhCchhEEEEEEEEEEECCEEEEEEEEEEcccCHHHHhcccccccccccccC
Confidence            998643 35899999999999999999999999999999999999999999999999999999999653322    2359


Q ss_pred             CCCCCCCeeeeeeeEEeeeecCCCCCCCHHHHHHHHH-----------------hcCCCCcCchhHHHHHhhcCCeEEEc
Q psy8714         462 PDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLME-----------------KHGIGTDASIPVHINNICQRNYVTVT  524 (562)
Q Consensus       462 p~l~~G~~~~~~~~~i~e~~TkPP~~~Te~~Li~~Me-----------------~~GIGTpATra~iI~~L~~r~Yi~~~  524 (562)
                      |.+++||.+.+.++.+.+++|+||+||||++||++||                 +.|||||||||+||++|++||||+. 
T Consensus       458 P~l~~G~~~~~~~~~~~~~~TkPP~ryTeasLi~~Me~~~k~v~d~~l~~~l~e~~GIGtpATrA~iI~~L~~R~Yv~~-  536 (660)
T TIGR01056       458 PAFQKGDELDVETLELLEKQTKPPARYTEGTLLSAMTNPAAFVQDKGLKKTLKETKGLGTEATRADIIENLFKRGFIQK-  536 (660)
T ss_pred             CCCCCCCEeeeeecccccCcCCCCCCcCHHHHHHHHHhhhhcccCHHHHHHhhhccCCCCcccHHHHHHHHHhCCCEEe-
Confidence            9999999999999999999999999999999999999                 7899999999999999999999997 


Q ss_pred             CCCeeecchhHHHHHHhhhccCccCCChhhHHHHHhhC
Q psy8714         525 SGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRVQA  562 (562)
Q Consensus       525 ~~k~l~~T~~G~~li~~l~~~~~~l~~p~~Ta~~E~~L  562 (562)
                      +|+.|+||++|+.|+++|.   +.|++|+|||.||.+|
T Consensus       537 ~~k~l~pT~~G~~v~~~L~---~~i~~~~~Ta~~E~~L  571 (660)
T TIGR01056       537 KKNKIYITKNGKLLCLLLP---ELLTKPDLTAQWEQYL  571 (660)
T ss_pred             eCCEEEEcHHHHHHHHHhH---HhcCChhHHHHHHHHH
Confidence            6789999999999999974   5799999999999876

This model describes topoisomerase III from bacteria and its equivalents encoded on plasmids. The gene is designated topB if found in the bacterial chromosome, traE on conjugative plasmid RP4, etc. These enzymes are involved in the control of DNA topology. DNA topoisomerase III belongs to the type I topoisomerases, which are ATP-independent.

>PRK07726 DNA topoisomerase III; Provisional

Probab=100.00  E-value=4.8e-127  Score=1074.28  Aligned_cols=528  Identities=25%  Similarity=0.394  Sum_probs=454.3

Q ss_pred             eEEEEecccCcCCcchHHhhcccccCCCCceeeeeeeeEcCCCcEEEEEEeccccccccccc----CCCCCccCCCCCCC
Q psy8714           6 KKLVPASEIKLARPSLISLLTPLQRMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTS----KYNNWDKVDPLELF   81 (562)
Q Consensus         6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~~~~~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~~~----~y~~W~~~~p~~~~   81 (562)
                      |+||||||     ||+|+.||.++|..+     ..+|||+|++  |+||||.|||++|+.|+    +|+.|+..++ ++.
T Consensus         1 ~~LiIaEK-----Ps~Ak~Ia~~L~~~~-----~~~g~~~g~~--~~Vt~~~GHl~~L~~p~~y~~~~~~W~~~~l-pi~   67 (658)
T PRK07726          1 MRLFIAEK-----PSVGRDIADVLKPHK-----KGDGYIEGNG--YIVTWAIGHLLELAEPEAYDERYKRWRLEDL-PII   67 (658)
T ss_pred             CeEEEEeC-----HHHHHHHHHHhCCcc-----CCCCeEeCCC--EEEEechhhhccCCCchhcccccCccccccC-CCC
Confidence            68999999     999999999998543     2479999874  78999999999997655    5567876542 121


Q ss_pred             CCCcccccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHHHHH
Q psy8714          82 SCPTEKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMW  161 (562)
Q Consensus        82 ~~~~~~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~A~~  161 (562)
                      +............++++.|++++++||+||||||||||||+|||+|+++++      +++||+|+|||++|+++|++||+
T Consensus        68 p~~~~~~~~~~~~~~~~~ik~l~~~~d~Ii~AtD~DREGE~I~~~i~~~~~------~~~~v~Rl~~sslt~~~I~~A~~  141 (658)
T PRK07726         68 PEKWKLVVKKKTAKQFNVVKKLLKQATEIVIATDADREGELIAREILDYCG------VRKPIKRLWISSLTDKAIKRAFA  141 (658)
T ss_pred             cccceeeeccchHHHHHHHHHHHhhCCeEEEcCCCCccccHHHHHHHHHhC------CCCCeEEEEEccCCHHHHHHHHH
Confidence            111111111223467788888889999999999999999999999999994      36899999999999999999999


Q ss_pred             hCCCCh--HhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhhhhhhhhhhcccCcceEEE
Q psy8714         162 NLVKPN--IFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLL  239 (562)
Q Consensus       162 nl~~~~--~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lIv~Re~eI~~F~p~~y~~i  239 (562)
                      ||++++  .+++.||.||+++|||||||+||++|+.+++.+.   ++++|+||||||||+|||+||++|+||+|++||+|
T Consensus       142 nl~~~~~~~~l~~aa~aR~~~D~liG~nlSr~~t~~~~~~g~---~~~lS~GRVQTPtL~lVv~Re~eI~~F~p~~y~~i  218 (658)
T PRK07726        142 NLKPGKETIPLYYSALARSRADWLVGINMTRAYTLLGRKAGY---NGVLSVGRVQTPTLALVVRRDEEIENFVPKPYWEV  218 (658)
T ss_pred             hcCCchhhHHHHHHHHHHHHHHHHhhhhHhHHHHHHHhhcCC---CcceeecccccchhHHHHHHHHHHHcCCCcccEEE
Confidence            999975  5889999999999999999999999998764321   34799999999999999999999999999999999


Q ss_pred             EEEEeeCCeEEEEEee--------cccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHHHHHHHHHhhCCC
Q psy8714         240 DLTLNLNGVAVSVTWS--------RGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGM  311 (562)
Q Consensus       240 ~~~~~~~~~~~~~~~~--------~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~  311 (562)
                      .+.+ .+|..|.+.|.        +++++|++.|+.+++.+.+ +.++|.+|++++++++||+||||++||++||++|||
T Consensus       219 ~~~~-~~~~~~~~~~~~~~~~~~~~~r~~~~~~a~~~~~~~~~-~~~~V~~v~~k~~~~~pP~pf~ls~Lq~~a~~~~g~  296 (658)
T PRK07726        219 EAHL-TPGERFTAKWQPSEPYQDEEGRLLDRPLAEQVVARIQG-QPAKVTEVETKRKKEYAPLLYDLSELQIDANKRFGL  296 (658)
T ss_pred             EEEE-cCCCeEEEEEeccccccccccccCCHHHHHHHHHHhcC-CCeEEEEEEeeEEecCCCCCCCHHHHHHHHHHhcCC
Confidence            9999 56678889995        3689999999999999975 479999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHhHhc-CceeecCCCCCCCCCcc--cHHHHHHHhccCCchhHHHHHHhhCCCCCCCC--CCCCCCCCCCc
Q psy8714         312 GPHHAMQIAERLYTQ-GYVSYPRTETTQYPENF--DLVAVLRQQESSPDWGDHVREVLSNGISKPRK--GKDVGDHPPIT  386 (562)
Q Consensus       312 s~~~tl~iaQ~LYE~-glISYPRTds~~l~~~~--~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~H~AI~  386 (562)
                      ||++||++||+|||+ ||||||||||++||+++  ++..+++.+.....|...+..++... .+.+.  .++++||||||
T Consensus       297 s~~~tl~iaQ~LYE~~glITYPRTds~~ls~~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~aH~AI~  375 (658)
T PRK07726        297 SAKETLDIAQSLYETHKLITYPRTDSRYLPEDMVATLPEVLNAISKVDPYLLLAPPVLDPS-IRSRAWNDKKVTAHHAII  375 (658)
T ss_pred             CHHHHHHHHHHHHHhcCEEEecCCCCccCCHHHHHHHHHHHHHHhccCcchhhhhhhhccc-cccCcCCCCcCCCCCCcC
Confidence            999999999999997 99999999999999986  57888888865555655444333221 12232  23458999999


Q ss_pred             cCCCcc-cCCCCHHHHHHHHHHHHHHHhhcccCceEEEEEEEEEECCeEEEEEEEEEeecceeeeecccccc---cCCCC
Q psy8714         387 PTKLAT-RTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMK---NESIP  462 (562)
Q Consensus       387 PT~~~~-~~~L~~~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~v~~~~~~~---~~~Lp  462 (562)
                      ||...+ ..+|+++|++||+||+|||||+|||||+|++|+|.+.++++.|.++|++++++||+.+|+.++.+   +..||
T Consensus       376 PT~~~~~~~~L~~~e~~iY~lI~~r~la~~~~~~~~~~t~v~~~~~~~~F~~~g~~i~~~Gw~~v~~~~~~~~~~~~~lp  455 (658)
T PRK07726        376 PTEQPPNLSKLSEDERKVYDLIARRYLAQFLPPAEYDKTTIELEIAGGTFIAKGKQVVEAGWKALLGKKEEDEEKEQPLP  455 (658)
T ss_pred             ccCCCCCcccCCHHHHHHHHHHHHHHHHHhCchhEEEEEEEEEEECCEEEEEEEEEEccCCHHHHcccccccccccccCC
Confidence            998643 35799999999999999999999999999999999999999999999999999999999653322   23599


Q ss_pred             CCCCCCeeeeeeeEEeeeecCCCCCCCHHHHHHHHHhc-----------------CCCCcCchhHHHHHhhcCCeEEEcC
Q psy8714         463 DFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKH-----------------GIGTDASIPVHINNICQRNYVTVTS  525 (562)
Q Consensus       463 ~l~~G~~~~~~~~~i~e~~TkPP~~~Te~~Li~~Me~~-----------------GIGTpATra~iI~~L~~r~Yi~~~~  525 (562)
                      .+++|+.+.+.++.+.+++|+||+||||++||++||+.                 |||||||||+||++|++||||.+ +
T Consensus       456 ~l~~g~~~~~~~~~~~e~~TkPP~~yTe~tLi~~Me~~~k~v~d~~~~~~l~e~~GIGTpATra~iIe~L~~R~Yi~~-~  534 (658)
T PRK07726        456 VLAKGDELKVEKGEVKEGQTQPPKRFTEGTLLSAMENIARFVQDKELKKTLKETDGLGTEATRAGIIEKLFKRGYLEK-K  534 (658)
T ss_pred             CcCCCCEeeecccccccccCCCCCCcCHHHHHHHHHhhhhhccCHHHHHhhcccCCCCccccHHHHHHHHHhCCCEEe-c
Confidence            99999999999999999999999999999999999875                 99999999999999999999997 6


Q ss_pred             CCeeecchhHHHHHHhhhccCccCCChhhHHHHHhhC
Q psy8714         526 GRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRVQA  562 (562)
Q Consensus       526 ~k~l~~T~~G~~li~~l~~~~~~l~~p~~Ta~~E~~L  562 (562)
                      |+.|+||++|+.|+++|.   ..|++|+|||.||.+|
T Consensus       535 ~k~l~pT~~G~~li~~l~---~~l~~p~~Ta~~E~~L  568 (658)
T PRK07726        535 GKYIHATDKGKQLIDALP---EELTSPDMTAKWEQAL  568 (658)
T ss_pred             CCEEEECHHHHHHHHHHH---HHcCChhhHHHHHHHH
Confidence            789999999999999874   4599999999999876

>TIGR01051 topA_bact DNA topoisomerase I, bacterial

Probab=100.00  E-value=6.9e-123  Score=1032.78  Aligned_cols=501  Identities=25%  Similarity=0.385  Sum_probs=432.7

Q ss_pred             EEEecccCcCCcchHHhhcccccCCCCceeeeeeeeEcCCCcEEEEEEecccccccccccCCCCCccCCCCCCCCCCccc
Q psy8714           8 LVPASEIKLARPSLISLLTPLQRMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPTEK   87 (562)
Q Consensus         8 l~~ae~~~~~~p~~a~~~~~~~g~~~~~~~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~~~~y~~W~~~~p~~~~~~~~~~   87 (562)
                      ||||||     ||+|+.|+.++|                +  .|+||||.|||++|..|+.|.+|...     |. |.. 
T Consensus         1 LiIaEk-----ps~a~~Ia~~lg----------------~--~~~Vt~~~GHl~~l~~~~~~~~~~~~-----~~-~~~-   50 (610)
T TIGR01051         1 LVIVES-----PAKAKTIKKYLG----------------D--EYEVEASMGHIRDLPKSRLGVDIEKD-----FE-PEY-   50 (610)
T ss_pred             CEEEeC-----hHHHHHHHHHhC----------------C--CCEEEeccCeeccCCCcccCCChhhc-----Cc-eeE-
Confidence            799999     999999998775                1  25799999999999877666677542     11 111 


Q ss_pred             ccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcE-EEEEecccCHHHHHHHHHhCCCC
Q psy8714          88 REATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTV-WRARFSAITDKDIKAAMWNLVKP  166 (562)
Q Consensus        88 ~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v-~Rl~~sslt~~~I~~A~~nl~~~  166 (562)
                      .....+.++++.|++++++||+||||||||||||+|||+|+++++      +++|+ +|+|||++|+++|++||+||+++
T Consensus        51 ~~~~~~~~~~~~i~~l~~~~d~ii~AtD~DrEGE~I~~~i~~~~~------~~~~~~~Rl~~s~lt~~~I~~a~~~l~~~  124 (610)
T TIGR01051        51 VVSKGKKKVVKELKTLAKKADEVYLATDPDREGEAIAWHLAEVLK------PKDPVYKRIVFNEITKKAIRAALKNPREI  124 (610)
T ss_pred             EEcccHHHHHHHHHHHHhcCCEEEECCCCCcchhHHHHHHHHHhC------CCCCCceEEEEccCCHHHHHHHHhCcccc
Confidence            111223467788888889999999999999999999999999995      34666 99999999999999999999999


Q ss_pred             hHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhhhhhhhhhhcccCcceEEEEEEEeeC
Q psy8714         167 NIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLN  246 (562)
Q Consensus       167 ~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lIv~Re~eI~~F~p~~y~~i~~~~~~~  246 (562)
                      +.++++||.||+++|||||||+||++|+.++        ..+|+||||||||+|||+||++|+||+|++||.|.+.+..+
T Consensus       125 ~~~l~~aa~aR~~~D~liG~n~Tr~~t~~~~--------~~lSvGRVQtPtL~lvv~Re~eI~~F~p~~y~~i~~~~~~~  196 (610)
T TIGR01051       125 DMNLVNAQQARRILDRLVGYTLSPLLWKKVA--------KGLSAGRVQSVALRLIVDREREIKRFVPEEYWTIDATFQKG  196 (610)
T ss_pred             chhHHHHHHHHHHHHHHHhHhhhHHHHHhhc--------CCCCcceehHHHHHHHHHHHHHHHhcCCCceEEEEEEEecC
Confidence            9999999999999999999999999998543        13999999999999999999999999999999999999877


Q ss_pred             CeEEEEEee--------cccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHHHHHHHHHhhCCCCHHHHHH
Q psy8714         247 GVAVSVTWS--------RGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQ  318 (562)
Q Consensus       247 ~~~~~~~~~--------~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl~  318 (562)
                      ++.|.+.|.        .++++|+++|+++++.+.+ +.++|.+|+.++++++||+||||++||++||++|||||++||+
T Consensus       197 ~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~-~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~S~~~tl~  275 (610)
T TIGR01051       197 EETFEALLTEVNGKKLKAGSDLDEAEATALKEQLKG-EELVVEEIEKKPKKSRPPPPFTTSTLQQEASRKLGFSAKKTMM  275 (610)
T ss_pred             CcceEEEEEecCCccccccccCCHHHHHHHHHHhcC-CCeEEEEEeeceeeeCCCCCcCHHHHHHHHHHhcCCCHHHHHH
Confidence            778888773        2478999999999999976 5789999999999999999999999999999999999999999


Q ss_pred             HHHHhHhc--------CceeecCCCCCCCCCcc--cHHHHHHHhccCCchhHHHHHHhhCCCCC-CCCCCCC-CCCCCCc
Q psy8714         319 IAERLYTQ--------GYVSYPRTETTQYPENF--DLVAVLRQQESSPDWGDHVREVLSNGISK-PRKGKDV-GDHPPIT  386 (562)
Q Consensus       319 iaQ~LYE~--------glISYPRTds~~l~~~~--~~~~~l~~l~~~~~~~~~~~~~~~~~~~~-~~~~~~~-~~H~AI~  386 (562)
                      +||+|||+        |+||||||||+|||+++  .+..+++.+..     .   .++.....+ +...+.+ +|||||+
T Consensus       276 iaQ~LYe~~~~~~~~~g~iSYPRTds~~l~~~~~~~~~~~l~~~~~-----~---~~~~~~~~~~~~~~k~~~~~H~aI~  347 (610)
T TIGR01051       276 IAQRLYEGVSTGDGTIGLITYMRTDSTRLSNQAVNEARNLIDKNYG-----K---EYLGPKPKRYKSKEKNAQEAHEAIR  347 (610)
T ss_pred             HHHHHHhcccccCCceeEEeecCcCccccCHHHHHHHHHHHHHhhh-----H---hhccccCcccCCCCCCCCCCcCCCC
Confidence            99999999        99999999999999975  35555554321     1   112111111 2222324 7899999


Q ss_pred             cCCCc--cc---CCCCHHHHHHHHHHHHHHHhhcccCceEEEEEEEEEE--CCeEEEEEEEEEeecceeeeeccccc---
Q psy8714         387 PTKLA--TR---TQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSV--ADEMFTMEAKYLLHPGFTGVMTWSAM---  456 (562)
Q Consensus       387 PT~~~--~~---~~L~~~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~--~~~~F~a~g~~~~~~Gw~~v~~~~~~---  456 (562)
                      ||...  +.   +.|+++|++||+||+|||||+|||||+|++|++.+.+  +++.|.++|++++++||+.+|+.+..   
T Consensus       348 Pt~~~~~~~~~~~~Ls~~e~~iY~lI~rr~la~~~~~~~~~~t~v~~~~~~~~~~F~a~g~~i~~~Gw~~v~~~~~~~~~  427 (610)
T TIGR01051       348 PTSVFRTPEELKDYLKRDEFRLYELIWKRFVASQMADARYDSTSVRLTNEDGEYVFKATGRKLIFDGYYKVYVEGSDDPL  427 (610)
T ss_pred             CCCCCcChhhhhccCCHHHHHHHHHHHHHHHHHhCccceEEEEEEEEEEcCCCeEEEEEEEEEEeCCHHHhccccccccc
Confidence            99763  22   4799999999999999999999999999999999999  99999999999999999999975422   


Q ss_pred             --ccCCCCCCCCCCeeeeeeeEEeeeecCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEcCCCeeecchh
Q psy8714         457 --KNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSL  534 (562)
Q Consensus       457 --~~~~Lp~l~~G~~~~~~~~~i~e~~TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~~~k~l~~T~~  534 (562)
                        ++..||.+++|+.+.+.++.+.+++|+||+||||++||++||+.|||||||||+||++|++||||.+ +|+.|+||++
T Consensus       428 ~~~~~~Lp~l~~g~~~~~~~~~~~~~~T~PP~~yTe~tLl~~Me~~GIGTpATra~iIe~L~~r~Yi~~-~~~~l~pT~~  506 (610)
T TIGR01051       428 EEKDRILPPLKEGDAVKLVEVKPNQHFTQPPARYTEASLVKELEELGIGRPSTYASIISTIQDRGYVKK-ENKRLYPTEL  506 (610)
T ss_pred             ccccccCCCCCCCCEeEeeeeeeccccccCCCCCCHHHHHHHHhcCCCCccccHHHHHHHHhhCCeEEe-eCCEEeECHH
Confidence              1345999999999999999999999999999999999999999999999999999999999999997 6789999999


Q ss_pred             HHHHHHhhhccCccCCChhhHHHHHhhC
Q psy8714         535 GIVLVHGYQKIDRELVEPTMRSAYRVQA  562 (562)
Q Consensus       535 G~~li~~l~~~~~~l~~p~~Ta~~E~~L  562 (562)
                      |+.|+++|....++|++|+|||.||..|
T Consensus       507 G~~li~~l~~~~~~l~~p~lTa~~E~~L  534 (610)
T TIGR01051       507 GFAVTDLLEKHFGDVVDYDFTAKMEKDL  534 (610)
T ss_pred             HHHHHHHHHHhhhhhcCHHHHHHHHHHH
Confidence            9999999977667899999999999876

This model describes DNA topoisomerase I among the members of bacteria. DNA topoisomerase I transiently cleaves one DNA strand and thus relaxes negatively supercoiled DNA during replication, transcription and recombination events.

>PRK05582 DNA topoisomerase I; Validated

Probab=100.00  E-value=4.7e-121  Score=1026.49  Aligned_cols=499  Identities=23%  Similarity=0.367  Sum_probs=429.0

Q ss_pred             eEEEEecccCcCCcchHHhhcccccCCCCceeeeeeeeEcCCCcEEEEEEecccccccccccCC----CC-CccCCCCCC
Q psy8714           6 KKLVPASEIKLARPSLISLLTPLQRMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKY----NN-WDKVDPLEL   80 (562)
Q Consensus         6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~~~~~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~~~~y----~~-W~~~~p~~~   80 (562)
                      +.||||||     ||+|+.|++++|.                  .|+|+||.|||++|..+ .+    .. |.   |  .
T Consensus         3 ~~LiIaEk-----ps~a~~ia~~lg~------------------~~~V~~~~GHl~~l~~~-~~~~~~~~~~~---~--~   53 (650)
T PRK05582          3 KKLVIVES-----PAKAKTIEKYLGK------------------NYKVVASMGHIRDLPKS-QLGIDIENNFE---P--K   53 (650)
T ss_pred             CeEEEEeC-----HHHHHHHHHHcCC------------------CCEEEeccCchhcCCCc-cCCCCcccCCc---e--e
Confidence            46999999     9999999987752                  26799999999999753 11    01 22   1  1


Q ss_pred             CCCCcccccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHHHH
Q psy8714          81 FSCPTEKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAM  160 (562)
Q Consensus        81 ~~~~~~~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~A~  160 (562)
                      |..      .....++++.|++++++||+||||||||||||+|||||+++++.    + .++++|+||||+|+++|++||
T Consensus        54 ~~~------~~~~~~~~~~ik~l~~~~d~ii~AtD~DrEGE~I~~~i~~~~~~----~-~~~~~R~~~s~lt~~~I~~a~  122 (650)
T PRK05582         54 YIT------IRGKGPVIKELKKAAKKAKKVYLATDPDREGEAIAWHLAHILGL----D-EKEKNRIVFNEITKDAIKNAF  122 (650)
T ss_pred             eEE------CCcHHHHHHHHHHHHhcCCEEEECCCCCcchHHHHHHHHHHhCC----C-CCCceEEEEcccCHHHHHHHH
Confidence            110      11223577888888899999999999999999999999999952    1 278899999999999999999


Q ss_pred             HhCCCChHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhhhhhhhhhhcccCcceEEEE
Q psy8714         161 WNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLD  240 (562)
Q Consensus       161 ~nl~~~~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lIv~Re~eI~~F~p~~y~~i~  240 (562)
                      +||++++.++++||.||+++||+||||+||++|+.+++        .+|+||||||||+|||+||++|+||+|++||+|.
T Consensus       123 ~nl~~~~~~l~~a~~aR~~~D~liG~n~tr~~t~~~~~--------~ls~GRVQtPtL~lvv~Re~eI~~F~p~~y~~i~  194 (650)
T PRK05582        123 KNPRKIDMNLVDAQQARRILDRLVGYKLSPLLWKKVKK--------GLSAGRVQSVALKLIIDREKEIRAFVPEEYWTID  194 (650)
T ss_pred             hCcccccHHHHHHHHHHHHHHHHhhhhcCHHHHHhhcC--------CCccccchHhHHHHHHhHHHHHHhCCCCccEEEE
Confidence            99999999999999999999999999999999986431        3899999999999999999999999999999999


Q ss_pred             EEEeeCCeEEEEEee-----cccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHHHHHHHHHhhCCCCHHH
Q psy8714         241 LTLNLNGVAVSVTWS-----RGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHH  315 (562)
Q Consensus       241 ~~~~~~~~~~~~~~~-----~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~  315 (562)
                      +.+..++..|.+.|.     .++++|+++|+++++.+.+ +.++|++|++++++.+||+||||++||++||++|||||++
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~-~~~~v~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~  273 (650)
T PRK05582        195 AEFKKGKKKFEASFYGYKGKKIELKNEEDVKEILAELKK-KDFKVSKVKKKERKRNPPPPFTTSTLQQEAARKLNFSTKK  273 (650)
T ss_pred             EEEecCCccEEEEEEecCCCccccCCHHHHHHHHHHhcC-CCeEEEEEeeeeeecCCCCCccHHHHHHHHHHHcCCCHHH
Confidence            999766666888763     4689999999999999976 5799999999999999999999999999999999999999


Q ss_pred             HHHHHHHhHh---------cCceeecCCCCCCCCCcc--cHHHHHHHhccCCchhHHHHHHhhCCCCCCCCCCCC-CCCC
Q psy8714         316 AMQIAERLYT---------QGYVSYPRTETTQYPENF--DLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDV-GDHP  383 (562)
Q Consensus       316 tl~iaQ~LYE---------~glISYPRTds~~l~~~~--~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~H~  383 (562)
                      ||++||+|||         +||||||||||++||+++  .+..++..+.     +   ..++.....+..+.+++ +|||
T Consensus       274 tl~~aQ~LYe~~~~~~~~~~gliSYPRTds~~l~~~~~~~~~~~~~~~~-----~---~~~~~~~~~~~~~~~k~~~~H~  345 (650)
T PRK05582        274 TMMIAQQLYEGIDLGKQGTVGLITYMRTDSTRISDTAQEEAREFIEEKY-----G---KEYLPKKPKVYKKKSGAQDAHE  345 (650)
T ss_pred             HHHHHHHHhcccccCCCCceEEEEecCCCcccCCHHHHHHHHHHHHHHh-----H---HHhhccCCcccCCCcCCCCCCC
Confidence            9999999999         699999999999999975  2445444321     1   11121111112233345 5899


Q ss_pred             CCccCCCc--cc---CCCCHHHHHHHHHHHHHHHhhcccCceEEEEEEEEEECCeEEEEEEEEEeecceeeeeccccccc
Q psy8714         384 PITPTKLA--TR---TQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKN  458 (562)
Q Consensus       384 AI~PT~~~--~~---~~L~~~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~v~~~~~~~~  458 (562)
                      ||+||...  +.   +.|+++|++||+||+|||||+|||||+|++|+|.++++++.|+++|++++++||+.+|+.++.++
T Consensus       346 aI~PT~~~~~p~~~~~~L~~~e~~iY~lI~~rfla~~~~~~~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~~~~~~~~~~  425 (650)
T PRK05582        346 AIRPTSVFLTPESAKKYLTKDQLKLYKLIWNRFVASQMAPAVFDTVSVDLENNGVKFRASGSKVKFDGFMKVYVGDEEKD  425 (650)
T ss_pred             CEeecCCCcChhHHhccCCHHHHHHHHHHHHHHHHHhCchhheeEEEEEEEeCCEEEEEEEEEEeeCChHhhcCCccccc
Confidence            99999862  22   47999999999999999999999999999999999999999999999999999999997433335


Q ss_pred             CCCCCCCCCCeeeeeeeEEeeeecCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEcCCCeeecchhHHHH
Q psy8714         459 ESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVL  538 (562)
Q Consensus       459 ~~Lp~l~~G~~~~~~~~~i~e~~TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~~~k~l~~T~~G~~l  538 (562)
                      ..||.+++|+.+.+.++.+.+++|+||+||||++||++||+.|||||||||+||++|++||||.. +|+.|+||++|+.|
T Consensus       426 ~~lp~l~~g~~~~~~~~~~~~~~T~PP~~~Te~~Ll~~Me~~GIGT~ATra~iI~~L~~r~Yi~~-~~k~l~pT~~G~~l  504 (650)
T PRK05582        426 KMLPELEEGEKVKLKKIEPEQHFTQPPARYTEASLIKTLEELGIGRPSTYAPTISTIQKRGYVKL-EKKRLVPTELGEIV  504 (650)
T ss_pred             ccCCCCCCCCEeEEEEeeecccccCCCCCCCHHHHHHHHHHcCCCCcccHHHHHHHHHhCCeEEe-eCCEEeecHHHHHH
Confidence            56999999999999999999999999999999999999999999999999999999999999997 67899999999999


Q ss_pred             HHhhhccCccCCChhhHHHHHhhC
Q psy8714         539 VHGYQKIDRELVEPTMRSAYRVQA  562 (562)
Q Consensus       539 i~~l~~~~~~l~~p~~Ta~~E~~L  562 (562)
                      +++|....++|++|+|||.||.+|
T Consensus       505 ~~~l~~~~~~l~~p~lTa~~E~~L  528 (650)
T PRK05582        505 NELLEEFFPDIVDVEFTAEMEEKL  528 (650)
T ss_pred             HHHHHHhchhhcCHHHHHHHHHHH
Confidence            999987777899999999999876

>PRK08780 DNA topoisomerase I; Provisional

Probab=100.00  E-value=2.3e-120  Score=1032.28  Aligned_cols=507  Identities=22%  Similarity=0.328  Sum_probs=430.6

Q ss_pred             eEEEEecccCcCCcchHHhhcccccCCCCceeeeeeeeEcCCCcEEEEEEecccccccccccCC-C-CCccCCCCCCCCC
Q psy8714           6 KKLVPASEIKLARPSLISLLTPLQRMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKY-N-NWDKVDPLELFSC   83 (562)
Q Consensus         6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~~~~~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~~~~y-~-~W~~~~p~~~~~~   83 (562)
                      |.||||||     |+.|+.|++.+|.                  .|+|+||.|||++|..|+.+ . .|. +.|  .|..
T Consensus         3 ~~LiIvEs-----PskAk~I~~~Lg~------------------~y~V~as~GHi~dL~~~~~~vd~~~~-f~~--~y~~   56 (780)
T PRK08780          3 KHLVIVES-----PAKAKTINKYLGK------------------DFTVLASYGHVRDLVPKEGAVDPENG-FAM--RYDL   56 (780)
T ss_pred             CeEEEEeC-----HHHHHHHHHHcCC------------------CCEEEeccCCcccCCCcccCCChhhC-Cce--EEEE
Confidence            67999999     9999999976552                  26799999999999755443 2 111 111  1111


Q ss_pred             CcccccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHHHHHhC
Q psy8714          84 PTEKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNL  163 (562)
Q Consensus        84 ~~~~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~A~~nl  163 (562)
                            ...+.++++.|++++++||+||||||||||||+|||||+++|+.. +....++|+|+|||+||+++|++||+|+
T Consensus        57 ------~~~k~~~~~~lk~~~k~ad~vilAtD~DREGE~Ia~~i~~~l~~~-~~~~~~~v~Ri~f~eiT~~aI~~A~~n~  129 (780)
T PRK08780         57 ------IDKNEKHVEAIAKAAKSADDLYLATDPDREGEAISWHLAEILKER-GLLKDKPMQRVVFTEITPRAIKEAMAKP  129 (780)
T ss_pred             ------cCchHHHHHHHHHHHHhCCEEEECCCCCcccHHHHHHHHHHhccc-ccCCCCceEEEEEccCCHHHHHHHHhCC
Confidence                  112346889999999999999999999999999999999999632 0011478999999999999999999999


Q ss_pred             CCChHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhhhhhhhhhhcccCcceEEEEEEE
Q psy8714         164 VKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTL  243 (562)
Q Consensus       164 ~~~~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lIv~Re~eI~~F~p~~y~~i~~~~  243 (562)
                      +++|+++++||+||+++|||||||+||++|..++        +.+|+||||||||+|||+||+||++|+|++||.|.+.+
T Consensus       130 r~~d~~l~~A~~aRr~lD~lvG~~lSr~l~~~~~--------~~lSaGRVQspaL~lIveRE~eI~~F~p~~yw~i~~~~  201 (780)
T PRK08780        130 RDIASDLVDAQQARRALDYLVGFNLSPLLWRKIQ--------RGLSAGRVQSPALRMIVEREEEIEAFIAREYWSIEADC  201 (780)
T ss_pred             CcCcHhHHHHHHHHHHHHHhcCeeecHHHHHhhC--------CCCcccccHHHHHHHHHHHHHHHHhCCCcceEEEEEEE
Confidence            9999999999999999999999999999997653        23899999999999999999999999999999999999


Q ss_pred             eeCCeEEEEEeec--------ccccCHHHHHHHHHHhhh--cCceEEEEEEcceeeccCCCCCCHHHHHHHHHhhCCCCH
Q psy8714         244 NLNGVAVSVTWSR--------GHIFDKSTCNVFFKAVEK--EKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGP  313 (562)
Q Consensus       244 ~~~~~~~~~~~~~--------~~~~~~~~a~~~~~~~~~--~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~  313 (562)
                      ..++..|.+.|..        .+++|+++|+++++.|.+  ...++|.+|++++++.+||+||+|++||++||++|||||
T Consensus       202 ~~~~~~f~a~~~~~~~~~~~~~~~~~~~~a~~i~~~~~~~~~~~~~V~~v~~k~~~~~pp~Pf~tstLQq~As~klg~s~  281 (780)
T PRK08780        202 AHPSQPFNAKLIKLDGQKFEQFTITDGDTAEAARLRIQQAAQGTLHVTDVESKERKRNPAPPFTTSTLQQEASRKLGFTT  281 (780)
T ss_pred             ecCCceEEEEEEecCCccccccccCCHHHHHHHHHHHhhccCCCeEEEEEEeeeeecCCCCCccHHHHHHHHHHHcCCCH
Confidence            8767778877742        368999999999999974  247899999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhHhc---------CceeecCCCCCCCCCcc--cHHHHHHHhccCCchhHHHHHHhhCCCCC-CCC-CCCCC
Q psy8714         314 HHAMQIAERLYTQ---------GYVSYPRTETTQYPENF--DLVAVLRQQESSPDWGDHVREVLSNGISK-PRK-GKDVG  380 (562)
Q Consensus       314 ~~tl~iaQ~LYE~---------glISYPRTds~~l~~~~--~~~~~l~~l~~~~~~~~~~~~~~~~~~~~-~~~-~~~~~  380 (562)
                      ++||++||+|||.         ||||||||||++||++.  ++...|..+....        .+...... +.+ .+..+
T Consensus       282 ~~Tm~iAQ~LYE~~~~~~~~~~glITYpRTDS~~ls~~~~~~~~~~i~~~~g~~--------~~~~~~~~~~~~~~~~q~  353 (780)
T PRK08780        282 RRTMQVAQKLYEGVDLGDEGSVGLITYMRTDSVNLSQDALAEIRDVIARDYGTA--------SLPDQPNTYKTKSKNAQE  353 (780)
T ss_pred             HHHHHHHHHHHhhcccccCCceeEEEecccCCccCCHHHHHHHHHHHHHHhChh--------hhhhcccccCCCCCCCcC
Confidence            9999999999997         99999999999999875  3455554432211        11111111 112 22347


Q ss_pred             CCCCCccCCCc--cc---CCCCHHHHHHHHHHHHHHHhhcccCceEEEEEEEEEECC-eEEEEEEEEEeecceeeeeccc
Q psy8714         381 DHPPITPTKLA--TR---TQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVAD-EMFTMEAKYLLHPGFTGVMTWS  454 (562)
Q Consensus       381 ~H~AI~PT~~~--~~---~~L~~~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~-~~F~a~g~~~~~~Gw~~v~~~~  454 (562)
                      ||||||||...  +.   ..|+++|++||+|||+||||+||+||+|++|+|.+.+++ +.|+++|++++++||+.+|...
T Consensus       354 aHeAI~PT~~~~~p~~~~~~L~~de~klY~LI~~R~lAs~m~~a~~~~t~v~~~~~~~~~F~a~G~~i~~~G~~~vy~~~  433 (780)
T PRK08780        354 AHEAVRPTSALRTPAQVARFLSDDQRRLYELIWKRAVACQMIPATLNTVSVDLAAGSEHVFRATGSTVVVPGFLAVYEEG  433 (780)
T ss_pred             CCCCCCCCCCCcChhhhhccCCHHHHHHHHHHHHHHHHHhCchhEEEEEEEEEEeCCeeEEEEEEEEEeEcCeEEeeccc
Confidence            79999999753  21   479999999999999999999999999999999999987 7999999999999999999653


Q ss_pred             cc----c--c--CCCCCCCCCCeeeeeeeEEeeeecCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEcCC
Q psy8714         455 AM----K--N--ESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSG  526 (562)
Q Consensus       455 ~~----~--~--~~Lp~l~~G~~~~~~~~~i~e~~TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~~~  526 (562)
                      ..    +  +  ..||.|++||.+.+.++.+.+++|+||+||||++||++||+.|||||||||+||++|++||||.. +|
T Consensus       434 ~~~~~~~~~~~~~~LP~l~~G~~~~~~~~~~~~~~T~PP~ryTEasLik~mE~~GIGtpST~A~iI~~L~~R~Yv~~-~~  512 (780)
T PRK08780        434 KDDKSAEDEDEGRKLPPMKEGDNVPLERIRAEQHFTEPPPRYTEASLVKALEEYGIGRPSTYASIISTLQFRKYVEM-EG  512 (780)
T ss_pred             cccccccccchhccCCCcCCCCEeeeeeeeeeeeecCCCCCCCHHHHHHHHHhCCCCchhhHHHHHHHHHhCCcEec-cC
Confidence            21    1  1  45999999999999999999999999999999999999999999999999999999999999997 67


Q ss_pred             CeeecchhHHHHHHhhhccCccCCChhhHHHHHhhC
Q psy8714         527 RRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRVQA  562 (562)
Q Consensus       527 k~l~~T~~G~~li~~l~~~~~~l~~p~~Ta~~E~~L  562 (562)
                      ++|+||++|+.|+++|...++.|+||+|||.||.+|
T Consensus       513 k~l~pT~~G~~v~~~L~~~f~~l~~~~~Ta~~E~~L  548 (780)
T PRK08780        513 RRFRPTDVGRAVNKFLTGHFTRYVDYDFTARLEDDL  548 (780)
T ss_pred             CEEeecHHHHHHHHHHHHhchhcCCHHHHHHHHHHH
Confidence            799999999999999988888999999999999876

>PRK07561 DNA topoisomerase I subunit omega; Validated

Probab=100.00  E-value=4e-120  Score=1042.97  Aligned_cols=506  Identities=26%  Similarity=0.400  Sum_probs=435.9

Q ss_pred             eEEEEecccCcCCcchHHhhcccccCCCCceeeeeeeeEcCCCcEEEEEEeccccccccc-----ccCCCC--Ccc--CC
Q psy8714           6 KKLVPASEIKLARPSLISLLTPLQRMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDF-----TSKYNN--WDK--VD   76 (562)
Q Consensus         6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~~~~~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~-----~~~y~~--W~~--~~   76 (562)
                      |.||||||     |+.|+.|++.+|                .  .|+|+||+|||++|..     |++|+.  |..  .+
T Consensus         2 ~~LvIvEk-----P~kak~I~~~Lg----------------~--~~~V~~s~GHi~dL~~~~~~~~~~~k~~~w~~l~i~   58 (859)
T PRK07561          2 KSLVIVES-----PAKAKTINKYLG----------------S--DYVVKASVGHIRDLPTSASSVPAKEKGALWARMGVD   58 (859)
T ss_pred             CEEEEEeC-----HHHHHHHHHHcC----------------C--CCEEEeccCChhhCCCccccChhhhhhchHhhcCcC
Confidence            68999999     999999997665                2  2679999999999975     455653  431  22


Q ss_pred             CCCCCCCCcccccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHH
Q psy8714          77 PLELFSCPTEKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDI  156 (562)
Q Consensus        77 p~~~~~~~~~~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I  156 (562)
                      |.+.|....  .....+.++++.|++++++||+||||||||||||+|||||+++++.     ++++|+|+|||+||+++|
T Consensus        59 ~~~~f~~~y--~~~~~k~~~~~~lk~~~k~ad~iilAtD~DREGE~I~~~i~~~l~~-----~~~~v~Ri~f~~iT~~aI  131 (859)
T PRK07561         59 PDHDFEALY--EVLPGKEKVVSELKKAAKDADELYLATDPDREGEAIAWHLLEVLGG-----DDVPVKRVVFNEITKNAI  131 (859)
T ss_pred             cccCcceeE--EECccHHHHHHHHHHHHhcCCEEEECCCCCccchHHHHHHHHHhCC-----CCCCeEEEEEccCCHHHH
Confidence            333332111  1112344789999999999999999999999999999999999952     368999999999999999


Q ss_pred             HHHHHhCCCChHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhhhhhhhhhhcccCcce
Q psy8714         157 KAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPY  236 (562)
Q Consensus       157 ~~A~~nl~~~~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lIv~Re~eI~~F~p~~y  236 (562)
                      ++||+|++++|.++++||+||+++|||||||+||++|..++        ..+|+||||||||+|||+||+||++|+|++|
T Consensus       132 ~~A~~n~~~~~~~l~~A~~aRr~lD~lvG~~lS~~l~~~~~--------~~lSaGRVQsp~L~lIv~Re~eI~~F~p~~y  203 (859)
T PRK07561        132 QEAFENPRELDINLVNAQQARRFLDRLVGYMVSPLLWKKIA--------RGLSAGRVQSVAVRLIVEREREIEAFVPEEY  203 (859)
T ss_pred             HHHHhCcccCCHHHHHHHHHHHHHHHHhhhhcCHHHHHhhc--------cCCCcccchhhhhHHHHHHHHHHHhcCCCcc
Confidence            99999999999999999999999999999999999987643        2399999999999999999999999999999


Q ss_pred             EEEEEEEee-CCeEEEEEeec--------ccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHHHHHHHHHh
Q psy8714         237 WLLDLTLNL-NGVAVSVTWSR--------GHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASS  307 (562)
Q Consensus       237 ~~i~~~~~~-~~~~~~~~~~~--------~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~  307 (562)
                      |.|.+.+.. +|..|.+.|..        .+++|+++|+++++.+.+ ..++|.+|+.++++.+||+||+|++||++||+
T Consensus       204 w~i~~~~~~~~~~~f~a~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~-~~~~V~~v~~k~~~~~pp~pf~ts~LQ~~As~  282 (859)
T PRK07561        204 WDIHADLTTPRGDAFEARLTHLDGKKFAPVDLLNEAQAEAAVAALEG-ARYSVASVEDKPTTRKPSAPFTTSTLQQEASR  282 (859)
T ss_pred             EEEEEEEEecCCCeEEEEEEeeCCceecccccCCHHHHHHHHHHhcC-CCeEEEEEEeceeEecCCCCccHHHHHHHHHH
Confidence            999999976 56678876631        247999999999999976 47899999999999999999999999999999


Q ss_pred             hCCCCHHHHHHHHHHhHhcCceeecCCCCCCCCCcc--cHHHHHHHhccCCchhHHHHHHhhCCCCCCCCC--C-C--CC
Q psy8714         308 GLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENF--DLVAVLRQQESSPDWGDHVREVLSNGISKPRKG--K-D--VG  380 (562)
Q Consensus       308 ~~g~s~~~tl~iaQ~LYE~glISYPRTds~~l~~~~--~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~--~-~--~~  380 (562)
                      +|||||++||++||+|||+||||||||||++||++.  ++..+|..+     |+.   .++.   ..+|.+  + +  .+
T Consensus       283 klg~s~~~tm~~aQ~LYE~glITYpRTDs~~ls~~~~~~~~~~i~~~-----~g~---~~~~---~~~r~~~~~~k~~q~  351 (859)
T PRK07561        283 KLGFSVKKTMRIAQRLYEAGYITYMRTDSTNLSQEAINAARGYIGDN-----YGK---KYLP---EKPRQYSSKAKNAQE  351 (859)
T ss_pred             hcCCCHHHHHHHHHHHHhCCeEEecCCCCCcCCHHHHHHHHHHHHHH-----hhh---hhcc---cCCccCCCcCCCCCC
Confidence            999999999999999999999999999999999874  355555543     221   1222   123332  1 2  26


Q ss_pred             CCCCCccCCCc--cc--CCCCHHHHHHHHHHHHHHHhhcccCceEEEEEEEEEECCeEEEEEEEEEeecceeeeeccccc
Q psy8714         381 DHPPITPTKLA--TR--TQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAM  456 (562)
Q Consensus       381 ~H~AI~PT~~~--~~--~~L~~~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~v~~~~~~  456 (562)
                      ||||||||...  +.  ..|+++|++||+|||+||||+||+||+|++|+|.+.++++.|+++|++++++||+.+|..+..
T Consensus       352 aHeAI~Pt~~~~~~~~~~~L~~~e~~lY~LI~~R~lAs~m~~a~~~~~~v~~~~~~~~F~a~g~~i~~~G~~~vy~~~~~  431 (859)
T PRK07561        352 AHEAIRPSDVFRTPDQLKGLEGDAQRLYELIWKRFVASQMAPARYDSTTVTIAAGDAELRATGRVLRFDGFLKVYVEGRD  431 (859)
T ss_pred             CcCCcccCCCCcChhhhccCCHHHHHHHHHHHHHHHHHhCchheEEEEEEEEEeCCEEEEEEEEEEeeCCchheeccccc
Confidence            79999999652  21  469999999999999999999999999999999999999999999999999999999975432


Q ss_pred             c-----cCCCCCCCCCCeeeeeeeEEeeeecCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEcCCCeeec
Q psy8714         457 K-----NESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGRRLVP  531 (562)
Q Consensus       457 ~-----~~~Lp~l~~G~~~~~~~~~i~e~~TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~~~k~l~~  531 (562)
                      +     +..||.+++|+.+.+.++.+.+++|+||+||||++||++||+.|||||||||+||++|++||||.. +|+.|+|
T Consensus       432 ~~~~~~~~~LP~l~~g~~~~~~~~~~~~~~T~PP~ryTeasLv~~me~~GIGtpsT~a~iI~~L~~R~Yv~~-~~~~l~p  510 (859)
T PRK07561        432 DALDDEDRRLPALKVGDALTLEKLDPTQHFTKPPARYSEASLVKELEKLGIGRPSTYASIISTIQDRGYVRL-ENRRFYP  510 (859)
T ss_pred             cccccccccCCCCCCCCEeeeeeeEecccccCCCCCCCHHHHHHHHHhcCCCcchhHHHHHHHHhhcCeEEe-eCCEEee
Confidence            1     346999999999999999999999999999999999999999999999999999999999999997 6789999


Q ss_pred             chhHHHHHHhhhccCccCCChhhHHHHHhhC
Q psy8714         532 TSLGIVLVHGYQKIDRELVEPTMRSAYRVQA  562 (562)
Q Consensus       532 T~~G~~li~~l~~~~~~l~~p~~Ta~~E~~L  562 (562)
                      |++|+.|+++|...++.|++|+|||.||..|
T Consensus       511 T~~G~~v~~~l~~~f~~l~~~~~Ta~~E~~L  541 (859)
T PRK07561        511 EKMGRIVTDRLEEFFPRLVDYDFTARMEEEL  541 (859)
T ss_pred             cHHHHHHHHHHHHhhhhhcCHHHHHHHHHHH
Confidence            9999999999988788999999999999876

>PRK06599 DNA topoisomerase I; Validated

Probab=100.00  E-value=1e-119  Score=1018.47  Aligned_cols=507  Identities=24%  Similarity=0.367  Sum_probs=430.7

Q ss_pred             eEEEEecccCcCCcchHHhhcccccCCCCceeeeeeeeEcCCCcEEEEEEecccccccccccCCCCCccCCCCCCCCCCc
Q psy8714           6 KKLVPASEIKLARPSLISLLTPLQRMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPT   85 (562)
Q Consensus         6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~~~~~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~~~~y~~W~~~~p~~~~~~~~   85 (562)
                      +.||||||     ||+|+.|+.++|.                  .|+|+||+|||++|.  +.+..|...+|   |. +.
T Consensus         3 ~~LiIaEK-----Ps~ak~Ia~~lg~------------------~~~V~~~~GHl~~l~--~~~~~~~~~~~---~~-~~   53 (675)
T PRK06599          3 KKLVIVES-----PAKAKTIKKYLGK------------------DYKVLASFGHVRDLP--KKKGGVDPDND---FA-PK   53 (675)
T ss_pred             CeEEEEeC-----HHHHHHHHHHcCC------------------CCEEEecccchhcCC--ccccCCCcccC---CC-ce
Confidence            46999999     9999999987752                  267999999999994  33445654332   21 11


Q ss_pred             ccccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHHHHHhCCC
Q psy8714          86 EKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNLVK  165 (562)
Q Consensus        86 ~~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~A~~nl~~  165 (562)
                      .. ....+.++++.|++++++||+||||||||||||+|||+|+++++..  .+.+++|+|+|||++|+++|++||+||++
T Consensus        54 ~~-~~~~~~~~~~~ik~l~~~~d~iiiAtD~DrEGE~I~~~i~~~~~~~--~~~~~~v~Rl~~s~lt~~~I~~a~~n~~~  130 (675)
T PRK06599         54 YE-IIEGKEKVVDALKKAAKKADAVYLATDPDREGEAIAWHIAEVLKEA--KLKDKNVKRVVFNEITKKAVQEAIENPRD  130 (675)
T ss_pred             EE-ECCcHHHHHHHHHHHHhhCCEEEECCCCCcchHHHHHHHHHHHHhh--cCCCCCeeEEEEccCCHHHHHHHHhCccc
Confidence            11 1122336788888888999999999999999999999999999521  02357999999999999999999999999


Q ss_pred             ChHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhhhhhhhhhhcccCcceEEEEEEEee
Q psy8714         166 PNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNL  245 (562)
Q Consensus       166 ~~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lIv~Re~eI~~F~p~~y~~i~~~~~~  245 (562)
                      ++.+++.||.||+++||+||||+||++|+.++        ..+|+||||||||+|||+||++|+||+|++||.|.+.+..
T Consensus       131 ~~~~l~~a~~aR~~~D~liG~n~tr~~t~~~~--------~~lS~GRVQtPtL~lvv~Re~eI~~F~p~~y~~i~~~~~~  202 (675)
T PRK06599        131 IDMDLVDAQQARRALDYLVGFKLSPLLWKKVR--------RGLSAGRVQSVALRLICEREDEIEAFIPQEYWTIEADLAT  202 (675)
T ss_pred             CCHHHHHHHHHHHHHHHHhhhhhCHHHHHhcc--------CCCccceeHHHHhHHHHHhHHHHHhcCCCceEEEEEEEEc
Confidence            99999999999999999999999999998763        2399999999999999999999999999999999999976


Q ss_pred             -CCeEEEEEeec------c--cccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHHHHHHHHHhhCCCCHHHH
Q psy8714         246 -NGVAVSVTWSR------G--HIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHA  316 (562)
Q Consensus       246 -~~~~~~~~~~~------~--~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~t  316 (562)
                       +|..|.+.|..      .  +++|+++|+++++.+.+ ..++|+++++++++++||+||||++||++||++|||||++|
T Consensus       203 ~~~~~~~~~~~~~~~~~~~~~r~~~~~~a~~~~~~~~~-~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~t  281 (675)
T PRK06599        203 SNGEPFTAKLVEVNGKKLEKFSITNEEQAKALVKALEG-QAYTVDKIEKKERKRNPPPPFITSTLQQEASRKLGFSAKKT  281 (675)
T ss_pred             CCCCeeEEEEEeccCccccccCCCCHHHHHHHHHHhcC-CCeEEEEEEeeEEecCCCCCCcHHHHHHHHHHHcCCCHHHH
Confidence             46678776531      1  69999999999999976 46899999999999999999999999999999999999999


Q ss_pred             HHHHHHhHhc--------CceeecCCCCCCCCCcc--cHHHHHHHhccCCchhHHHHHHhhCCCCCCCC-CCCC-CCCCC
Q psy8714         317 MQIAERLYTQ--------GYVSYPRTETTQYPENF--DLVAVLRQQESSPDWGDHVREVLSNGISKPRK-GKDV-GDHPP  384 (562)
Q Consensus       317 l~iaQ~LYE~--------glISYPRTds~~l~~~~--~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~-~~~~-~~H~A  384 (562)
                      |++||+|||+        ||||||||||+|||+++  ++..+++.+.. ..       ++.......++ .+.+ +||||
T Consensus       282 l~~aQ~LYe~~~~~~~~~g~iSYPRTds~~l~~~~~~~~~~~l~~~~~-~~-------~~~~~~~~~~~~~~~~~~aH~a  353 (675)
T PRK06599        282 MRIAQKLYEGIDLGEGTVGLITYMRTDSVRLSNEALDEARKYITKKYG-KE-------YLPAKPRVYKKKSKNAQEAHEA  353 (675)
T ss_pred             HHHHHHHHhccccccccceeEEeccCCCccCCHHHHHHHHHHHHHHhc-hh-------hccccCcccCCCCCCCCCCCCC
Confidence            9999999995        99999999999999875  35566655422 11       11101111112 2223 77999


Q ss_pred             CccCCCc--cc---CCCCHHHHHHHHHHHHHHHhhcccCceEEEEEEEEEE--CCeEEEEEEEEEeecceeeeecccccc
Q psy8714         385 ITPTKLA--TR---TQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSV--ADEMFTMEAKYLLHPGFTGVMTWSAMK  457 (562)
Q Consensus       385 I~PT~~~--~~---~~L~~~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~--~~~~F~a~g~~~~~~Gw~~v~~~~~~~  457 (562)
                      |+||...  +.   +.|+++|++||+||+|||||+|||||+|++|+|.+.+  +++.|.++|++++++||+.+|++++.+
T Consensus       354 I~Pt~~~~~~~~~~~~l~~~e~~iY~lI~~rfla~~~~~~~~~~t~v~~~~~~~~~~F~a~g~~~~~~Gw~~~~~~~~~~  433 (675)
T PRK06599        354 IRPTSINRTPESLKPYLTPDQFKLYELIWKRTVASQMAPAILDQTSVDIASENGKYVFRATGSVILFPGFLKVYGESKDD  433 (675)
T ss_pred             CccCCCCCChhHhhccCCHHHHHHHHHHHHHHHHHhCchheEEEEEEEEEEcCCCeEEEEEEEEEEecCeeeeecccccc
Confidence            9999862  21   4799999999999999999999999999999999999  999999999999999999999764321


Q ss_pred             -----cCCCCCCCCCCeeeeeeeEEeeeecCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEcCCCeeecc
Q psy8714         458 -----NESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPT  532 (562)
Q Consensus       458 -----~~~Lp~l~~G~~~~~~~~~i~e~~TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~~~k~l~~T  532 (562)
                           +..||.+++||.+.+.++.+.+++|+||+||||++||++||+.|||||||||+||++|++||||.+ +|+.|+||
T Consensus       434 ~~~~~~~~lp~~~~g~~~~~~~~~~~~~~T~PP~r~te~tLi~~Me~~GIGT~ATra~iIe~L~~r~Yi~~-~~~~l~~T  512 (675)
T PRK06599        434 EEEDDEKLLPPLKEGEKLKLDELLPEQHFTEPPPRYSEASLVKKLEEYGIGRPSTYASIISTLQDREYVEL-EKKRFIPT  512 (675)
T ss_pred             ccccccccCCCCCCCCEeeeeeeeecccccCCCCCCCHHHHHHHHhhCCCCccccHHHHHHHHhhCCeEEe-eCCEEeec
Confidence                 345999999999999999999999999999999999999999999999999999999999999997 57799999


Q ss_pred             hhHHHHHHhhhccCccCCChhhHHHHHhhC
Q psy8714         533 SLGIVLVHGYQKIDRELVEPTMRSAYRVQA  562 (562)
Q Consensus       533 ~~G~~li~~l~~~~~~l~~p~~Ta~~E~~L  562 (562)
                      ++|+.|+++|....+.|++|+|||.||..|
T Consensus       513 ~~G~~l~~~l~~~~~~l~~p~lTa~~E~~L  542 (675)
T PRK06599        513 DLGRIVNDFLVEHFPKYVDYDFTAGLEDEL  542 (675)
T ss_pred             HHHHHHHHHHHHhchhhCCHHHHHHHHHHH
Confidence            999999999876667899999999999875

>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated

Probab=100.00  E-value=2.4e-119  Score=1034.21  Aligned_cols=502  Identities=23%  Similarity=0.334  Sum_probs=432.2

Q ss_pred             eEEEEecccCcCCcchHHhhcccccCCCCceeeeeeeeEcCCCcEEEEEEecccccccccccCCCCCccCCCCCCCCCCc
Q psy8714           6 KKLVPASEIKLARPSLISLLTPLQRMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPT   85 (562)
Q Consensus         6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~~~~~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~~~~y~~W~~~~p~~~~~~~~   85 (562)
                      |.||||||     |+.|+.|++.+|                .  .|+|+|+.|||++|  |+++..|...++   |. |.
T Consensus         3 ~~LvIvEs-----P~kak~I~~~Lg----------------~--~~~V~as~GHl~dL--p~~~~~~~~~~~---f~-p~   53 (860)
T PRK06319          3 KSLIIVES-----PAKIKTLQKLLG----------------E--GFIFASSLGHIVDL--PAKEFGIDIEND---FE-PD   53 (860)
T ss_pred             CeEEEEeC-----HHHHHHHHHHhC----------------C--CCEEEecccCcccC--CcccCCcCCCCC---CC-cc
Confidence            68999999     999999997665                2  26799999999999  666656765432   21 11


Q ss_pred             ccccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHHHHHhCCC
Q psy8714          86 EKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNLVK  165 (562)
Q Consensus        86 ~~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~A~~nl~~  165 (562)
                      .. ....+.++++.|++++++||.||||||||||||+|+|||+++++      .+++|+|+|||++|+++|++||+|+++
T Consensus        54 y~-~~~~k~~~~~~ik~~~k~ad~iilAtDpDREGE~I~~~i~~~l~------~~~~v~Rv~f~~iT~~aI~~A~~~~~~  126 (860)
T PRK06319         54 YQ-ILPDKEEVINKICKLAKKCDVVYLSPDPDREGEAIAWHIANQLP------KNTKIQRISFNAITKGAVTEALKHPRE  126 (860)
T ss_pred             eE-ECccHHHHHHHHHHHHHhCCEEEECCCCCcchHHHHHHHHHHcC------CCCCeeEEEEccCCHHHHHHHHhCccc
Confidence            10 11223468899999999999999999999999999999999994      358999999999999999999999999


Q ss_pred             ChHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhhhhhhhhhhcccCcceEEEEEEEee
Q psy8714         166 PNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNL  245 (562)
Q Consensus       166 ~~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lIv~Re~eI~~F~p~~y~~i~~~~~~  245 (562)
                      +|+++++||+||+++|||||||+||++|..++..      ..+|+||||||||+|||+||+||+||+|++||+|.+.+..
T Consensus       127 ~d~~l~~A~~aR~~lD~lvG~nlSr~l~~~~~~~------~~lSaGRVQsp~L~lIveRe~eI~~F~p~~yw~i~~~~~~  200 (860)
T PRK06319        127 IDMALVNAQQARRLLDRIVGYKISPILSRKLQRR------SGVSAGRVQSVALKLVVDREKAIEAFVPVEYWNIRVHLKD  200 (860)
T ss_pred             cCHHHHHHHHHHHHHHHHhhhhcCHHHHHhhccC------CCCcCCccchhhhHHHHHHHHHHHcCCCCceEEEEEEEec
Confidence            9999999999999999999999999999876532      2499999999999999999999999999999999999875


Q ss_pred             C--CeEEEEEeec-------------------ccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHHHHHHH
Q psy8714         246 N--GVAVSVTWSR-------------------GHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRV  304 (562)
Q Consensus       246 ~--~~~~~~~~~~-------------------~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~  304 (562)
                      +  +..|.+.|..                   .++.|+++|+++++.+++ ..++|++|++++++.+||+||+|++||++
T Consensus       201 ~~~~~~f~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~i~~~l~~-~~~~V~~v~~k~~~~~pp~pf~ts~LQ~~  279 (860)
T PRK06319        201 PKTQKTFWAHLYSVDGKKWEKEIPEGKTEDEVLLINSKEKADHIVELLES-ATYTVTRVESKEKRRNAYPPFITSTLQQE  279 (860)
T ss_pred             CCCCcceEEEeecccCcccccccccccccccccccCCHHHHHHHHHHhcC-CCeEEEEEEeeEeecCCCCCccHHHHHHH
Confidence            3  4568777631                   137899999999999976 47999999999999999999999999999


Q ss_pred             HHhhCCCCHHHHHHHHHHhHhc---------CceeecCCCCCCCCCcc--cHHHHHHHhccCCchhHHHHHHhhCCCCCC
Q psy8714         305 ASSGLGMGPHHAMQIAERLYTQ---------GYVSYPRTETTQYPENF--DLVAVLRQQESSPDWGDHVREVLSNGISKP  373 (562)
Q Consensus       305 a~~~~g~s~~~tl~iaQ~LYE~---------glISYPRTds~~l~~~~--~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~  373 (562)
                      ||++|||||++||++||+|||.         ||||||||||++||++.  ++..+|..+..     .   .++.   ..+
T Consensus       280 As~~~g~sa~~tm~iAQ~LYE~~~~~~~~~~glITYpRTDs~~ls~~~~~~~~~~i~~~~g-----~---~~~~---~~~  348 (860)
T PRK06319        280 ASRHFRFSSSRTMNIAQTLYEGVDLDSEGATGLITYMRTDSVRTDPEALKQVRKYIEGTFG-----K---EFLP---SSP  348 (860)
T ss_pred             HHHHcCCCHHHHHHHHHHHHhccccccCCceeEEeecCcCcccCCHHHHHHHHHHHHHhhh-----h---hhcc---cCC
Confidence            9999999999999999999994         99999999999999875  35555554321     1   1221   122


Q ss_pred             CC--CCCC--CCCCCCccCCCc--cc---CCCCHHHHHHHHHHHHHHHhhcccCceEEEEEEEEEECC-eEEEEEEEEEe
Q psy8714         374 RK--GKDV--GDHPPITPTKLA--TR---TQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVAD-EMFTMEAKYLL  443 (562)
Q Consensus       374 ~~--~~~~--~~H~AI~PT~~~--~~---~~L~~~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~-~~F~a~g~~~~  443 (562)
                      +.  .+++  +||||||||...  +.   ..|+++|++||+|||+||||+||+||+|++|+|.+.+++ +.|+++|++++
T Consensus       349 ~~~~~~k~~q~aH~AI~PT~~~~~p~~~~~~L~~de~klY~LI~~RflAs~m~~a~~~~t~v~~~~~~~~~F~a~G~~i~  428 (860)
T PRK06319        349 NVYTTKKMAQDAHEAIRPTDITLTPEKLRSKLTEDQYKLYSLIWKRFVASQMIPAIYDTLAIRITTNKGIDLRATGSLLK  428 (860)
T ss_pred             cccCCCCCCCCCcCCCccCCCCcChhHhhccCCHHHHHHHHHHHHHHHHHhCchhheEEEEEEEEeCCeeEEEEEeEEEe
Confidence            22  2223  579999999853  22   479999999999999999999999999999999999987 68999999999


Q ss_pred             ecceeeeeccccc------ccCCCCCCCCCCeeeeeeeEEeeeecCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhc
Q psy8714         444 HPGFTGVMTWSAM------KNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQ  517 (562)
Q Consensus       444 ~~Gw~~v~~~~~~------~~~~Lp~l~~G~~~~~~~~~i~e~~TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~  517 (562)
                      ++||++||..+..      ++..||.|++||.+.+.++.+.+++|+||+||||++||++||+.|||||||||+||++|++
T Consensus       429 ~~G~~~vy~~~~~~~~~~~~~~~LP~l~~Ge~~~~~~~~~~~~~T~PP~ryTeasLvk~me~~GIGtpsT~A~iI~~L~~  508 (860)
T PRK06319        429 FKGFLAVYEEKRDDEGDEEENIHLPKLHEQDVLTKEELSAEQAFTKPLPRFTEASLVKELEKSGIGRPSTYATIMNKIQS  508 (860)
T ss_pred             eCCHHHHhCccccccccccccccCCCCCCCCEeeeeeeeecccccCCCCCCCHHHHHHHHHhcCCCchhhHHHHHHHHhh
Confidence            9999999964321      1346999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCeEEEcCCCeeecchhHHHHHHhhhccCccCCChhhHHHHHhhC
Q psy8714         518 RNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRVQA  562 (562)
Q Consensus       518 r~Yi~~~~~k~l~~T~~G~~li~~l~~~~~~l~~p~~Ta~~E~~L  562 (562)
                      ||||.. +|++|+||++|+.|+++|...++.|++|+|||.||.+|
T Consensus       509 R~Yv~~-~~k~l~pT~~G~~v~~~L~~~f~~i~~~~~Ta~~E~~L  552 (860)
T PRK06319        509 REYTLK-ENQRLRPTELGKIISQFLETNFPRIMDIGFTALMEDEL  552 (860)
T ss_pred             CCeEEc-cCCEEEECHHHHHHHHHHHHhchhhcChhHHHHHHHHH
Confidence            999997 57799999999999999988788999999999999876

>PTZ00407 DNA topoisomerase IA; Provisional

Probab=100.00  E-value=3.7e-112  Score=947.12  Aligned_cols=531  Identities=20%  Similarity=0.297  Sum_probs=412.7

Q ss_pred             ceEEEEecccCcCCcchHHhhcccccCCCCceeeeee-eeEc----CCCcEEEEEEecccccccccccCCCCCccC--C-
Q psy8714           5 VKKLVPASEIKLARPSLISLLTPLQRMNGACSVHEWV-GPLF----GDLVLFKMTSVCGHIMGLDFTSKYNNWDKV--D-   76 (562)
Q Consensus         5 ~~~l~~ae~~~~~~p~~a~~~~~~~g~~~~~~~~~~~-g~~~----g~~~~~~Vt~~~GHl~~l~~~~~y~~W~~~--~-   76 (562)
                      .-+|+|+|+     |...=.+.-.++-.+-++-+.|. +++-    |.. .-+..++-||+|.|..-    .|...  . 
T Consensus         9 ~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~----~~~~~~~~~   78 (805)
T PTZ00407          9 LEKLVIVES-----PNKVIKVEGLLSDPKVIPDWSFKQSHLRRIGTGAE-KAVAMATTGHFMALKEI----TWSPQASSP   78 (805)
T ss_pred             hhheeEEec-----CCceEEEeecccCCCcCCCcccccccceeeccchH-HHHHHhhcccceeehhe----ecccCCCCC
Confidence            468999999     44433333333445555656663 2332    221 23466888999998521    23321  0 


Q ss_pred             ------CCCCCC--------CCcccccCCCC-CchHH-HHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCC
Q psy8714          77 ------PLELFS--------CPTEKREATPK-LKLPA-FLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSP  140 (562)
Q Consensus        77 ------p~~~~~--------~~~~~~~~~~~-~~~i~-~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~  140 (562)
                            +.+-|+        .|........+ .++|. .|++++++||+||+|||||||||+|+|||+++++... ..++
T Consensus        79 ~~~~~~~~~~~~~~~~~~~f~~~y~~~~~~~~~~~i~~~i~~~ak~ad~IIlATDpDREGE~Ia~hIle~l~~~~-~~~~  157 (805)
T PTZ00407         79 ASVVGAGDEPFPSNGTLAEYTLEWELLPGRRIQETLERYIEEKADNVTEIILATDPDREGELIAVHALQTIKRLY-PKLK  157 (805)
T ss_pred             cccCCCCCCCCCCCCceEEEEEEEEEcCCCchhHHHHHHHHHHHhcCCEEEECCCCCcchHHHHHHHHHHhchhc-cccC
Confidence                  111122        01111111111 14565 6999999999999999999999999999999996420 0135


Q ss_pred             CcEEEEEecccCHHHHHHHHHhC--CCChHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccch
Q psy8714         141 KTVWRARFSAITDKDIKAAMWNL--VKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTL  218 (562)
Q Consensus       141 ~~v~Rl~~sslt~~~I~~A~~nl--~~~~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL  218 (562)
                      ++++|+|||++|+++|++||+|+  ++++.++++|+.||+++|||||||+||+++...        .+.+|+||||||||
T Consensus       158 k~v~Rv~FseITk~aI~~A~~nlkp~~~d~~L~~Aa~ARr~lD~LVG~nlS~~l~~~~--------~~~lSaGRVQTPtL  229 (805)
T PTZ00407        158 VPFSRAYMHSITEDGIRKAMRERHVEACDYDLANAAETRHAMDRIFGFLGSSVVRAAN--------SQMRSIGRVQTPAL  229 (805)
T ss_pred             CcceEEEEccCCHHHHHHHHhCCCCCcccHhHHHHHHHHHHHHHHhhhhhhHHHHhhc--------cCceeecccchHHH
Confidence            78999999999999999999995  668889999999999999999999999987631        23699999999999


Q ss_pred             hhhhhhhhhhhcccCc--ceEEEEEEEee---CCeEEEEEee--------cccccCHHHHHHHHHHhh--hcCceEEE-E
Q psy8714         219 GFCVERHDKIRTFKPE--PYWLLDLTLNL---NGVAVSVTWS--------RGHIFDKSTCNVFFKAVE--KEKHVTVV-D  282 (562)
Q Consensus       219 ~lIv~Re~eI~~F~p~--~y~~i~~~~~~---~~~~~~~~~~--------~~~~~~~~~a~~~~~~~~--~~~~~~V~-~  282 (562)
                      +|||+||+||++|+|+  +||.|.+.+..   +|..|.+.|.        +.++.|+++|+++++.++  +...++|. .
T Consensus       230 ~LIVeRE~EIe~Fkpee~~Yw~I~a~~~~~~~~g~~F~a~~~~~~~~~~~~~~~~~~~eA~~~~~~~~~~~~~~~~V~~~  309 (805)
T PTZ00407        230 ILINEREDKIKAFLESNKSTFEVQAMCQFPSPHGTTFSQVVTITPDRKGGASHWATEAEARRCLEQWKLNNCTGFSVPLE  309 (805)
T ss_pred             HHHHHHHHHHHhcCCccCceEEEEEEEeecCCCCcceeEEeeccccccccccccCCHHHHHHHHHHhhhccCCcEEEEEE
Confidence            9999999999999999  69999988752   3566776653        135778999999988764  22346664 4


Q ss_pred             EEcceeeccCCCCCCHHHHHHHHHhhCCCCHHHHHHHHHHhHhcCceeecCCCCCCCCCcc--cHHHHHHHhccCCchhH
Q psy8714         283 VQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENF--DLVAVLRQQESSPDWGD  360 (562)
Q Consensus       283 v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl~iaQ~LYE~glISYPRTds~~l~~~~--~~~~~l~~l~~~~~~~~  360 (562)
                      +++++++++||+||||++||++||++|||||++||++||+|||.||||||||||++||+++  ++.+.|...     ++.
T Consensus       310 v~~k~kk~~PP~PF~tstLQqeAsrkLG~Sa~kTM~iAQ~LYE~GlITYPRTDS~~l~~e~~~~i~~~I~~~-----~g~  384 (805)
T PTZ00407        310 PKPQPSVVPPPQPFTMATAIAKANRQLKYSSEMVSGCLQDLFQLGHITYPRTDSTRIDESALPDIYAAVKKE-----FGK  384 (805)
T ss_pred             EEEEEEEcCCCCCccHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCceeccCCCCCcCCHHHHHHHHHHHHHh-----hhh
Confidence            6678999999999999999999999999999999999999999999999999999999986  344444431     221


Q ss_pred             HHHHHh----------hCCCCCCC--------CC----C---CCC-CCCCCccCCCccc---CCCCHHHHHHHHHHHHHH
Q psy8714         361 HVREVL----------SNGISKPR--------KG----K---DVG-DHPPITPTKLATR---TQLDGDAWRLYDYIVRHF  411 (562)
Q Consensus       361 ~~~~~~----------~~~~~~~~--------~~----~---~~~-~H~AI~PT~~~~~---~~L~~~e~~vY~lI~rr~  411 (562)
                         .++          ......++        .+    .   +++ |||||+||+....   ..|+++|++||+||||||
T Consensus       385 ---~~l~~~~~~~~~~~~~~~~~k~~k~~~~~~k~~~d~~~~kvqeAHeAIrPT~~~~~~~~~~Ls~de~kLYdLI~rRf  461 (805)
T PTZ00407        385 ---EFLYRLEDRTVSAQEGKGSKKTGKKRSTKQKKGADTPVGNVEDAHEAIRPTNIDTTGESLSLSPPTRAVYDLVRRNT  461 (805)
T ss_pred             ---hhhhhhcccccccccccccccccccccccccccccccccCCCCCcCCCCccCCCCChhhccCCHHHHHHHHHHHHHH
Confidence               111          10001111        11    1   444 7999999986432   269999999999999999


Q ss_pred             HhhcccCceEEEEEEEEEEC-----CeEEEEEEEEEeecceeeeecccc----------c------c--cCCCCCCCCCC
Q psy8714         412 IGTLCGDLVYTQKVAKFSVA-----DEMFTMEAKYLLHPGFTGVMTWSA----------M------K--NESIPDFKPGD  468 (562)
Q Consensus       412 la~~~~~a~~~~t~v~~~~~-----~~~F~a~g~~~~~~Gw~~v~~~~~----------~------~--~~~Lp~l~~G~  468 (562)
                      ||+||+||+|++|++.+.+.     ++.|+++|++++++||++||++..          .      +  +..||.+++||
T Consensus       462 LAs~m~~a~~e~t~v~i~~~~~~g~~~~F~asGk~v~~~Gw~~vy~~~~~~~~~~~~e~~e~~~~~~e~~~~LP~l~~Gd  541 (805)
T PTZ00407        462 LAVFMIPMKTEKIVATVKFTSGSGEKLEFELQGKRVVEPGWTRAFHKGDKGTTGPAEETDEDITAVEEGAPVVPSLSQEE  541 (805)
T ss_pred             HHHhCchhEEEEEEEEEEEeccCCCceEEEEEEEEEeeCCHHHHhcccccccccccccccccccccccccccCCcccCCc
Confidence            99999999999999998873     358999999999999999996321          0      1  13599999998


Q ss_pred             ------------------eeeeeeeEEeeeecCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEcCCCeee
Q psy8714         469 ------------------LIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGRRLV  530 (562)
Q Consensus       469 ------------------~~~~~~~~i~e~~TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~~~k~l~  530 (562)
                                        .+.+.++.+.+++|+||+||||++||++||+.|||||||||+||++|++||||.++.|++|+
T Consensus       542 ~~~~~~~~~~~g~~~~q~~~~i~~~~l~ek~TkPPpryTEAtLIk~ME~~GIGTPATrAsIIetL~~R~YV~~~~kkrl~  621 (805)
T PTZ00407        542 FKAIMNLRSQLGSGVQKGFFELRSPQVRENRPVPPLPHSEGTLIEELKNNGVGRPSTYPMIVKTLLARGYIAVNPKGRCE  621 (805)
T ss_pred             cccccccccccccccccceeecceeeeecccCCCCCCCCHHHHHHHHHhCCCCCcccHHHHHHHHHhcCCEEeccCceee
Confidence                              35567889999999999999999999999999999999999999999999999983277899


Q ss_pred             cchhHHHHHHhhhccCccCCChhhHHHHHhhC
Q psy8714         531 PTSLGIVLVHGYQKIDRELVEPTMRSAYRVQA  562 (562)
Q Consensus       531 ~T~~G~~li~~l~~~~~~l~~p~~Ta~~E~~L  562 (562)
                      ||++|+.|+++|...++.|++|+|||.||.+|
T Consensus       622 PT~lG~~Li~~L~~~fp~lv~p~~TA~~E~~L  653 (805)
T PTZ00407        622 TTPVGRMLVETAKSTFPSIVDIGFTAAFEKKL  653 (805)
T ss_pred             ecHHHHHHHHHHHHhhhhhcChHHHHHHHHHH
Confidence            99999999999988888999999999999986

>PRK09401 reverse gyrase; Reviewed

Probab=100.00  E-value=4.8e-112  Score=994.95  Aligned_cols=504  Identities=22%  Similarity=0.296  Sum_probs=421.6

Q ss_pred             eEEEEecccCcCCcchHHhhcccccCCCCceeeeeeeeEc---CCCcEEEEEEecccccccccccCCCCCccCC-CC-CC
Q psy8714           6 KKLVPASEIKLARPSLISLLTPLQRMNGACSVHEWVGPLF---GDLVLFKMTSVCGHIMGLDFTSKYNNWDKVD-PL-EL   80 (562)
Q Consensus         6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~~~~~~~~~g~~~---g~~~~~~Vt~~~GHl~~l~~~~~y~~W~~~~-p~-~~   80 (562)
                      +.||||||     |++|+.||+++|....... ++-.+|+   |+. .++||||.|||++|..|++|..|...+ |. +.
T Consensus       602 ~~LiIaEk-----PskAk~IA~~lg~~~~r~~-g~~~~ye~~~~~~-~~~Vt~s~GHl~dL~~~~~y~g~~~~~~p~~P~  674 (1176)
T PRK09401        602 TTLLIVES-----PTKARTIANFFGRPSRRRI-GGLVVYETVTGDR-ILTITASKGHVYDLTTEIGYYGVLVKDGGFVPV  674 (1176)
T ss_pred             CEEEEEcC-----HHHHHHHHHHhCCCccccC-CCceeEEEecCCc-EEEEEEeccccccCCCccccCcccccCCcccce
Confidence            57999999     9999999999987532111 1111244   543 358999999999999999998898644 21 11


Q ss_pred             CCC------------------Ccc-cccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCC
Q psy8714          81 FSC------------------PTE-KREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPK  141 (562)
Q Consensus        81 ~~~------------------~~~-~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~  141 (562)
                      |..                  |.. .....++.++++.|++++++||+||||||||||||+|||+|+++++.     +++
T Consensus       675 y~~~k~c~~~g~~f~~~~~~~~~c~~~~~~~k~~~~~~Lr~l~~~~d~IiiAtDpDrEGE~Ia~~i~~~l~~-----~~~  749 (1176)
T PRK09401        675 YDTIKRCRDCGYQFTDESDKCPRCGSTNIEDKEEIIEALRELALEVDEVLIATDPDTEGEKIAWDLYLLLSP-----YNS  749 (1176)
T ss_pred             eeeeccccccccccccccccccccccccCCCHHHHHHHHHHHHhcCCEEEEccCcChhHHHHHHHHHHHhcc-----cCC
Confidence            210                  000 00113345788999999999999999999999999999999999963     358


Q ss_pred             cEEEEEecccCHHHHHHHHHhCCCChHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhh
Q psy8714         142 TVWRARFSAITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFC  221 (562)
Q Consensus       142 ~v~Rl~~sslt~~~I~~A~~nl~~~~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lI  221 (562)
                      +|+|+|||++|+++|++||+|++++|.+++.||.||+++||+||||+||++|+.+++       ..+|+||||||||+||
T Consensus       750 ~i~R~~f~eiT~~aI~~A~~n~r~~~~~l~~A~~aRr~~D~~iG~~lSr~l~~~~~~-------~~lSaGRVQTPtL~~I  822 (1176)
T PRK09401        750 NIKRIEFHEVTRKAILEALRNPRDVNENLVKAQIVRRIEDRWIGFELSQKLQKKFGK-------RNLSAGRVQTPVLGWI  822 (1176)
T ss_pred             CEEEEEeecCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc-------cCccccccccchhhhh
Confidence            999999999999999999999999999999999999999999999999999986542       2499999999999999


Q ss_pred             hhhhhhhhcccCcceEEEEEEEeeCCeEEEEEeecccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHHHH
Q psy8714         222 VERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVEL  301 (562)
Q Consensus       222 v~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~L  301 (562)
                      |+|++||++|++  ||.+ ... .+|..|.+.+   ++.+++.|+.+.+.+.     +|.+++.++++.+||+||||++|
T Consensus       823 VeRe~ei~~f~~--~~~~-~~~-~~~~~~~~~~---~~~~~~~a~~~~~~l~-----~V~~v~~k~~~~~pP~Pf~t~~L  890 (1176)
T PRK09401        823 VERYKEYKKSKG--YVLV-IKL-ENGGGLELEG---EFSEKEEAEKFYNNLI-----EVEKVEEKEEELNPLPPYTTDTL  890 (1176)
T ss_pred             hhhHHHhcccCC--EEEE-EEe-cCCceEEEEE---eeCCHHHHHHHHHhCC-----eeeEEEeeEEEecCCCCCccHHH
Confidence            999999999975  4444 332 3455566653   6889999999888774     78999999999999999999999


Q ss_pred             HHHHHhhCCCCHHHHHHHHHHhHhcCceeecCCCCCCCCCcc-c-HHHHHHHhccCCchhHHHHHHhhCCCCCCCCCCCC
Q psy8714         302 MRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENF-D-LVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDV  379 (562)
Q Consensus       302 q~~a~~~~g~s~~~tl~iaQ~LYE~glISYPRTds~~l~~~~-~-~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~  379 (562)
                      |++||++|||||++||++||+|||+||||||||||+++|++. + +...+..+..             ....+||.+.++
T Consensus       891 q~~As~~lg~Sa~~tm~iAQ~LYE~glITYpRTDS~~ls~~~~~~a~~~l~~~~~-------------~~~~~~r~~~~~  957 (1176)
T PRK09401        891 LSDASRKLRLSAQETMRIAQDLFELGLITYHRTDSTRVSDVGISVAKEYLEKRGG-------------EEYFVPRSWGEG  957 (1176)
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHhCCceeecCCCCCcCCHHHHHHHHHHHHHhhC-------------ccccCCCCCCCC
Confidence            999999999999999999999999999999999999999864 2 3344443321             122467887778


Q ss_pred             CCCCCCccCCCccc---------------CCCCHHHHHHHHHHHHHHHhhcccCceEEEEEEEEEECCeEEEEE-EEEEe
Q psy8714         380 GDHPPITPTKLATR---------------TQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTME-AKYLL  443 (562)
Q Consensus       380 ~~H~AI~PT~~~~~---------------~~L~~~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~~~F~a~-g~~~~  443 (562)
                      +||||||||...+.               ..|+++|++||+||+|||||+||+||+|++|++.+.++++.|.++ |++++
T Consensus       958 ~aH~AI~PT~~~~~~~l~~~~~~g~~~~~~~Lt~~e~~lY~LI~rRflAs~~~~a~~~~t~v~~~~~~~~f~~~~g~~i~ 1037 (1176)
T PRK09401        958 GAHEAIRPTRPLDAEELRQMIEEGILKLSEGLTKNHLRLYDLIFRRFMASQMKPAKVRYQKVLIKADGKELELELVVEIL 1037 (1176)
T ss_pred             CCcCCcCccCCCCchhhhhhhccccccccccCCHHHHHHHHHHHHHHHHHhCchhEEEEEEEEEEECCEEEEEeeeeEEe
Confidence            99999999985331               468999999999999999999999999999999999999999999 99999


Q ss_pred             ecceeeeecccccccCCCCCCCCCCeeeeeeeEEeeeecCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEE
Q psy8714         444 HPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTV  523 (562)
Q Consensus       444 ~~Gw~~v~~~~~~~~~~Lp~l~~G~~~~~~~~~i~e~~TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~  523 (562)
                      ++||+.+|+..     .+|.++.|+.+..    ++.++|.||+||||++||++||+.|||||||||+||++|++||||..
T Consensus      1038 ~~Gw~~v~~~~-----~~p~~~~g~~~~~----~~~~~~~pp~~yTea~Li~~Me~~GIGtpAT~A~IIe~L~~R~YV~~ 1108 (1176)
T PRK09401       1038 EDGFNKVLPLK-----LYPLLEGKVKVKE----KKTYKKSKVPLYTQGDLISEMKERGIGRPSTYAKIVETLLRRGYVIE 1108 (1176)
T ss_pred             eCChheeeccc-----cCCCCCCCCEeee----eccccCCCcCCCCHHHHHHHHHhCCCCCcCcHHHHHHHHhccCcEEE
Confidence            99999999643     3889999998864    45556666999999999999999999999999999999999999985


Q ss_pred             cCC-CeeecchhHHHHHHhhhccCccCCChhhHHHHHhhC
Q psy8714         524 TSG-RRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRVQA  562 (562)
Q Consensus       524 ~~~-k~l~~T~~G~~li~~l~~~~~~l~~p~~Ta~~E~~L  562 (562)
                      .+| +.|+||++|+.++++|....+.+++|++||.||..|
T Consensus      1109 ~~~~k~l~pT~~G~~l~~~L~~~~~~l~s~e~Ta~~E~~l 1148 (1176)
T PRK09401       1109 SKGKKRLIPTKLGIKVYEYLSEKYKDLVSEERTRKLEEKM 1148 (1176)
T ss_pred             cCCcceEeECHHHHHHHHHHHHhhhhcCCHHHHHHHHHHH
Confidence            344 589999999999999976667899999999999875

>KOG1956|consensus

Probab=100.00  E-value=2.6e-112  Score=894.43  Aligned_cols=553  Identities=38%  Similarity=0.669  Sum_probs=513.1

Q ss_pred             eEEEEecccCcCCcchHHh-----hcccccCCCCceeeeeeeeEcCCCcEEEEEEecccccccccccCCCCCccCCCCCC
Q psy8714           6 KKLVPASEIKLARPSLISL-----LTPLQRMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLEL   80 (562)
Q Consensus         6 ~~l~~ae~~~~~~p~~a~~-----~~~~~g~~~~~~~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~~~~y~~W~~~~p~~~   80 (562)
                      +-|++|||.+ .+.++|..     .+.+.|.++++++|.|+..+.|++++.++|+..|||+++++|.+|..|..+.|..+
T Consensus         2 ~vl~vAekn~-~ak~va~il~~g~~~~re~rSk~~kiy~f~~~~~g~~~~~~mtsvsghl~~~~f~~~~s~w~s~~~~~l   80 (758)
T KOG1956|consen    2 RVLCVAEKNS-IAKSVASILSGGTVRRREGRSKYNKIYDFDFNLFGQNCDVTMTSVSGHLTEADFPSEYSKWQSCPPDEL   80 (758)
T ss_pred             Ccccccccch-hhhhhhhhcCCCCcCCccchhhhhhhhhhhhhhcCCcceeEEeeccccccccCCcccccceeecCHHHH
Confidence            3589999932 22334443     56677889999999998888899999999999999999999999999999999999


Q ss_pred             CCCCcccccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHHHH
Q psy8714          81 FSCPTEKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAM  160 (562)
Q Consensus        81 ~~~~~~~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~A~  160 (562)
                      |..|..+.....+..+.+.|++++++||.+|||||||||||+|||||.+.|+.+   +....|.|+.||+||+.+|+.|.
T Consensus        81 f~a~~~~~~~~~~~~i~~~ir~eAr~ad~LviwtDcDREGE~Ig~eI~~v~~~~---~~~~~V~RA~Fs~it~~~I~sA~  157 (758)
T KOG1956|consen   81 FDAPVIKSVPENAKDIAKTIREEARRADYLVIWTDCDREGENIGWEIIDVCRAV---KRLLQVRRARFSEITRSAIKSAA  157 (758)
T ss_pred             hhhhhhhcCchhhhHHHHHHHHHHhhcceEEEeccCCccchhhhHHHHHHHHhh---CccceeehhhhhcccHHHHHHHH
Confidence            988877666666777889999999999999999999999999999999999876   55567999999999999999999


Q ss_pred             HhCCCChHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhhhhhhhhhhcccCcceEEEE
Q psy8714         161 WNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLD  240 (562)
Q Consensus       161 ~nl~~~~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lIv~Re~eI~~F~p~~y~~i~  240 (562)
                      +||+++|+.+++|..||+++|++||..|||++|+.+++++.-+..+++|+|+||+|||++||||+++|++|+|+.||+|.
T Consensus       158 ~nlreid~~~v~AvdaR~ELDlrIGa~FTRlqT~~L~r~f~~~~~~viSyG~cQfpTLgfVvdR~~eIe~FvPEefWtl~  237 (758)
T KOG1956|consen  158 RNLREIDEKLVHAVDARIELDLRIGAAFTRLQTLLLRRKFPILGEQVISYGPCQFPTLGFVVDRYKEIENFVPEEFWTLK  237 (758)
T ss_pred             hCccccchHHHHHHHHHHHHHHHhhhhHHHHHhHHHHhhhhhhhccccccccccCcceeeeeehHHHHhccCCcceEEEE
Confidence            99999999999999999999999999999999999988776444689999999999999999999999999999999999


Q ss_pred             EEEeeCCeEEEEEeecccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHHHHHHHHHhhCCCCHHHHHHHH
Q psy8714         241 LTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIA  320 (562)
Q Consensus       241 ~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl~ia  320 (562)
                      ......++...+.|.+++++|...+--+.+.|...+.+.|+++.++++++.||+||+|.+||+.|+++|.||+++||+||
T Consensus       238 ~~~~~~~~~~~fnw~R~~lfdr~s~~~~~e~c~e~k~a~Vv~~~kkpktKyrP~pl~TvELqK~~s~~lrlSak~TM~iA  317 (758)
T KOG1956|consen  238 FKHTHKGGLTEFNWKRGHLFDRLSVVILYEICVEEKEATVVKVTKKPKTKYRPLPLDTVELQKLASRKLRLSAKHTMKIA  317 (758)
T ss_pred             EEEeccCceeEEeecccccccHHHHHHHHHHHhcccceeEEecccCCccCCCCCcchHHHHHhhhhhheeccHHHHHHHH
Confidence            99988899999999999999999999999999888899999999999999999999999999999999999999999999


Q ss_pred             HHhHhcCceeecCCCCCCCCCcccHHHHHHHhccCCchhHHHHHHhhCCCCCCCCCCCC-CCCCCCccCCCcc-cCCCCH
Q psy8714         321 ERLYTQGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDV-GDHPPITPTKLAT-RTQLDG  398 (562)
Q Consensus       321 Q~LYE~glISYPRTds~~l~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~H~AI~PT~~~~-~~~L~~  398 (562)
                      ++||.+|+||||||++..+|.++++..+++.+...+.|+.+|..++..+...||++++. .||++|+||.... ...++.
T Consensus       318 E~ly~~gfisyprtetd~F~s~~~lk~lv~~qt~~~~wg~yA~~ll~~~~r~Prng~~~d~Ahppihp~k~~s~~~~~s~  397 (758)
T KOG1956|consen  318 EKLYQKGFISYPRTETDNFPSDMDLKALVEKQTQDPAWGSYAQRLLQPENRNPRNGKHNDKAHPPIHPTKFTSREANLSG  397 (758)
T ss_pred             HHHHhccceeccccccccCCCcCchHHHHHhhccCchhHHHHHHhhccCCCCCCCCccccccCCCccceeeccccccCCc
Confidence            99999999999999999999999999999999989999999999988655689998765 7899999998644 357999


Q ss_pred             HHHHHHHHHHHHHHhhcccCceEEEEEEEEEECCeEEEEEEEEEeecceeeeecccccccCCCCCCCCCCeeeeeeeEEe
Q psy8714         399 DAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKMV  478 (562)
Q Consensus       399 ~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~v~~~~~~~~~~Lp~l~~G~~~~~~~~~i~  478 (562)
                      |+++||++|+||||||.+.||+-..|+|+++++.+.|.++|..+++.+|..||++++|++..||.++.|+.+.+..+++.
T Consensus       398 d~~~vye~v~rhflAc~S~dakg~et~vel~~~~E~F~asgl~vl~~NyldVy~yekwe~k~Lp~y~~ge~fq~~~lem~  477 (758)
T KOG1956|consen  398 DHRKVYELVVRHFLACCSQDAKGAETTVELDIAQERFSASGLRVLERNYLDVYPYEKWEDKQLPVYEDGELFQPGELEMK  477 (758)
T ss_pred             chHHHHHHHHHHHHHhhcccccccceEEEEeehhhhccccccchhhccccccccccccccccCcccccccccccceEEec
Confidence            99999999999999999999999999999999999999999999999999999999999889999999999999999999


Q ss_pred             eeecCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEE-cCCCeeecchhHHHHHHhhhccCccCCChhhHHH
Q psy8714         479 ERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTV-TSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSA  557 (562)
Q Consensus       479 e~~TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~-~~~k~l~~T~~G~~li~~l~~~~~~l~~p~~Ta~  557 (562)
                      ++.|.||++|||++||+.|+++||||+||.|+||++|+.|+||.+ .+..+|.||.+|.+|+++|+.++-++++|.+||.
T Consensus       478 ~g~T~~P~~ltEaeLI~lMdk~GIGtdAT~aehi~kiq~R~Yv~~~~~~~~~~P~~lg~aLv~gyd~~g~e~sKp~lra~  557 (758)
T KOG1956|consen  478 DGETSPPKYLTEAELISLMDKNGIGTDATIAEHIEKIQERGYVTKKNKVGRFVPTFLGVALVEGYDDMGLEMSKPFLRAE  557 (758)
T ss_pred             cCccCCCCccCHHHHHHHHHHcCCCCchhHHHHHHHHHhhcceeeeccccccCchHHHHHHHHhHHhhhhhcCChHHHHH
Confidence            999999999999999999999999999999999999999999987 3334688999999999999999999999999999


Q ss_pred             HHhhC
Q psy8714         558 YRVQA  562 (562)
Q Consensus       558 ~E~~L  562 (562)
                      ||.+|
T Consensus       558 mE~~L  562 (758)
T KOG1956|consen  558 MEVDL  562 (758)
T ss_pred             HHHHH
Confidence            99876

>TIGR01054 rgy reverse gyrase

Probab=100.00  E-value=2.2e-109  Score=973.54  Aligned_cols=503  Identities=20%  Similarity=0.272  Sum_probs=418.0

Q ss_pred             eEEEEecccCcCCcchHHhhcccccCCC-----CceeeeeeeeEcCCCcEEEEEEecccccccccccCCCCCccCC-CC-
Q psy8714           6 KKLVPASEIKLARPSLISLLTPLQRMNG-----ACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVD-PL-   78 (562)
Q Consensus         6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~-----~~~~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~~~~y~~W~~~~-p~-   78 (562)
                      ..||||||     |+.|+.||.++|...     ..++|+|.+   |+. .++||||.|||++|..|+.|..|...+ |. 
T Consensus       602 ~~LiIvEs-----P~kAk~Ia~~lg~~~~r~~~g~~~yE~~~---g~~-~~~Vtas~GHl~dL~~~~~~~g~~~~~~~f~  672 (1171)
T TIGR01054       602 TALLVVES-----PNKARTIARFFGKPSVRKIGGSVVYEVPV---GDL-ILMITASGGHVFDLVTDKGFHGVLVENGRYV  672 (1171)
T ss_pred             ceEEEEcC-----hHHHHHHHHHhCCCcccccCCcceEEEec---CCe-eEEEEEeCceeeeCCCccccCcccccCCccc
Confidence            57999999     999999999998752     222333321   443 468999999999998887776776533 11 


Q ss_pred             CCCC------------------CCcc-cccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCC
Q psy8714          79 ELFS------------------CPTE-KREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININS  139 (562)
Q Consensus        79 ~~~~------------------~~~~-~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~  139 (562)
                      +.|.                  +|.. .....++.++++.|++++++||+||||||||||||+|||+|++++++     +
T Consensus       673 P~y~~~k~~~~~~~~f~~~~~~~p~~~~~~~~~k~~~~~~lr~l~~~~d~ViiATDpDrEGE~Ia~~i~~~l~~-----~  747 (1171)
T TIGR01054       673 PVYTSIKRCRDCGYQFTEDRESCPKCGSENIEDSKSIIEILRELAHEVDEVFIGTDPDTEGEKIGWDLALLLSP-----Y  747 (1171)
T ss_pred             ccccccccCCchhhhccccccccccccccccccHHHHHHHHHHHHhcCCEEEECCCCCccHHHHHHHHHHHhcc-----c
Confidence            1111                  0100 00113345788999999999999999999999999999999999863     3


Q ss_pred             CCcEEEEEecccCHHHHHHHHHhCCCChHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchh
Q psy8714         140 PKTVWRARFSAITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLG  219 (562)
Q Consensus       140 ~~~v~Rl~~sslt~~~I~~A~~nl~~~~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~  219 (562)
                      +++|+|+|||++|+++|++||+|++++|.++++||.||+++||+||||+||++|+.+++       +.+|+||||||||+
T Consensus       748 ~~~i~R~~f~eiT~~aI~~A~~n~r~~~~~L~~A~~aRr~~D~liG~~lSr~lt~~~~~-------~~lSaGRVQTPtL~  820 (1171)
T TIGR01054       748 NPNVKRAEFHEVTRRAILEALESPRSVDENLVKAQVVRRIEDRWIGFTLSQKLWEAFNK-------RWLSAGRVQTPVLG  820 (1171)
T ss_pred             CCCeEEEEEccCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhhhhCHHHHHhhcC-------CCcccceecchhhH
Confidence            67999999999999999999999999999999999999999999999999999975532       35999999999999


Q ss_pred             hhhhhhhhhhcccCcceEEEEEEEeeCCeEEEEEeecccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHH
Q psy8714         220 FCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTV  299 (562)
Q Consensus       220 lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~  299 (562)
                      |||+|++||++|+  +||.+.+..  ++..+...|     .+++.|+++.+.+.   .++|.+++.++++.+||+||+|+
T Consensus       821 lIVeRe~ei~~~~--~~~~i~~~~--~~~~~~~~~-----~~~~~a~~~~~~~~---~~~V~~v~~k~~~~~pP~Pf~t~  888 (1171)
T TIGR01054       821 WIIDRYRESREKR--GYLLIFALE--SDFRLGLEH-----DNRLEAKEFEKDLT---WLDVEDIAEREEERNPLPPYTTD  888 (1171)
T ss_pred             HHHHHHHHHhCCC--ceEEEEEec--CCeEEEEEe-----CCHHHHHHHHHhCC---CcEEEEEEeeEEeccCCCCCCHH
Confidence            9999999999965  589887643  233344333     57888888888773   57899999999999999999999


Q ss_pred             HHHHHHHhhCCCCHHHHHHHHHHhHhcCceeecCCCCCCCCCcc--cHHHHHHHhccCCchhHHHHHHhhCCCCCCCCCC
Q psy8714         300 ELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENF--DLVAVLRQQESSPDWGDHVREVLSNGISKPRKGK  377 (562)
Q Consensus       300 ~Lq~~a~~~~g~s~~~tl~iaQ~LYE~glISYPRTds~~l~~~~--~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~  377 (562)
                      +||++||++|||||++||++||+|||+||||||||||+++|++.  .+.+.+..+             +......||.+.
T Consensus       889 ~Lq~~As~~lg~sa~~tm~iAQ~LYE~GlITYpRTDS~~ls~~~~~~~~~~l~~~-------------~~~~~~~~r~~~  955 (1171)
T TIGR01054       889 TMLEDANRKLGLSVKETMQIAQELFENGLITYHRTDSTRVSDVGMRVAKEYLASR-------------LGGEYFYPREWG  955 (1171)
T ss_pred             HHHHHHHHhcCCCHHHHHHHHHHHHhCCEEEecCCCCCcCCHHHHHHHHHHHHHH-------------hcccccCCCCCC
Confidence            99999999999999999999999999999999999999999864  233333321             111123577777


Q ss_pred             CCCCCCCCccCCCccc--------------CCCCHHHHHHHHHHHHHHHhhcccCceEEEEEEEEEECC-eEEEEEEEEE
Q psy8714         378 DVGDHPPITPTKLATR--------------TQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVAD-EMFTMEAKYL  442 (562)
Q Consensus       378 ~~~~H~AI~PT~~~~~--------------~~L~~~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~-~~F~a~g~~~  442 (562)
                      +.+|||||+||...+.              ..|+++|++||+||+|||||+||+||+|+++++.+.+++ +.|.++|+++
T Consensus       956 ~~~aHeAI~PT~~~~~~~l~~~~~~g~~~~~~Ls~~e~~lY~LI~rRflAs~~~~a~~~~t~v~~~~~~~~~f~~~g~~i 1035 (1171)
T TIGR01054       956 EGGAHECIRPTRPLDVDDLQRLILEGVIELEGLTREHLRLYDLIFRRFMASQMRPAKVDTKEITLKADGKEAEEEGIVEI 1035 (1171)
T ss_pred             CCCCcCCcCCcCCCChhhhhhhhcccccccccCCHHHHHHHHHHHHHHHHHhCchheEEEEEEEEEeCCeeEEEEEEEEE
Confidence            7789999999986331              368999999999999999999999999999999999966 7999999999


Q ss_pred             eecceeeeecccccccCCCCCCCCCCeeeeeeeEEeeeecCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEE
Q psy8714         443 LHPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVT  522 (562)
Q Consensus       443 ~~~Gw~~v~~~~~~~~~~Lp~l~~G~~~~~~~~~i~e~~TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~  522 (562)
                      +++||+.+|+.+.     .+.+.+|+.+.+.+..+.++.  ||+||||++||++||+.|||||||||+||++|++||||.
T Consensus      1036 ~~~Gw~~v~~~~~-----~~~~~~G~~~~~~~~~~~~~~--~~p~yTe~~Li~~Me~~GIGtpsT~A~II~~L~~R~YV~ 1108 (1171)
T TIGR01054      1036 VERGFELVYPLWR-----KNELEKGSTFIVKDKELRSVP--KVYPYTQGEIVQEMKERGIGRPSTYATIVEKLLRRGYVV 1108 (1171)
T ss_pred             eeCCHHHHcCccc-----cccccCCCEeeeecceeeecC--CCCCCCHHHHHHHHHhCCCCCcccHHHHHHHhhccCcEE
Confidence            9999999997533     445788999988777776654  445999999999999999999999999999999999998


Q ss_pred             EcCCCeeecchhHHHHHHhhhccCccCCChhhHHHHHhhC
Q psy8714         523 VTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRVQA  562 (562)
Q Consensus       523 ~~~~k~l~~T~~G~~li~~l~~~~~~l~~p~~Ta~~E~~L  562 (562)
                      . +++.|+||++|+.|++.|....+.|++|++||.||..|
T Consensus      1109 ~-~~k~l~pT~lG~~v~~~L~~~~~~l~~~~~Ta~~E~~L 1147 (1171)
T TIGR01054      1109 E-SKGFLIPTKLGIEVYNYLTNRYPKLVSEDRTRELEEAM 1147 (1171)
T ss_pred             e-eCCEEeECHHHHHHHHHHHhhhhhcCCHhHHHHHHHHH
Confidence            6 66799999999999999977667899999999999875

Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA.

>PF01131 Topoisom_bac: DNA topoisomerase; InterPro: IPR013497 DNA topoisomerases regulate the number of topological links between two DNA strands (i

Probab=100.00  E-value=2.8e-95  Score=777.77  Aligned_cols=380  Identities=31%  Similarity=0.549  Sum_probs=301.8

Q ss_pred             ChHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhhhhhhhhhhcccCcceEEEEEEEee
Q psy8714         166 PNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNL  245 (562)
Q Consensus       166 ~~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lIv~Re~eI~~F~p~~y~~i~~~~~~  245 (562)
                      .+.+++.||.||+++|||||||+||++|   .       .+++|+||||||||+|||+||++|+||+|++||.|.+.+..
T Consensus         2 ~~~~l~~a~~aR~~~D~liG~n~Sr~~t---~-------~~~ls~GRVQtp~L~li~~Re~ei~~f~~~~y~~i~~~~~~   71 (403)
T PF01131_consen    2 EDKNLYNAAEARQEADWLIGMNLSRALT---G-------NGVLSVGRVQTPTLGLIVEREREIENFKPEPYYEIKAQFKK   71 (403)
T ss_dssp             -GHHHHHHHHHHHHHHHHHHHHHHHHHH---H-------STT-TTHTTHHHHHHHHHHHHHHHHCEEEEEEEEEEEEEET
T ss_pred             CCHhHHHHHHHHHHHHHhcChhcCHhhc---C-------CCccccCcccchHHHHHHHHHhhhhccCCCceEEEEEEecc
Confidence            5778999999999999999999999997   1       24799999999999999999999999999999999999876


Q ss_pred             CCeEEEEEeecccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHHHHHHHHHhhCCCCHHHHHHHHHHhHh
Q psy8714         246 NGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYT  325 (562)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl~iaQ~LYE  325 (562)
                      ++.. ...+.+.++.|+++|+.+++.+...   .|.+++.++++.+||+||||++||++||++|||||++||++||+|||
T Consensus        72 ~~~~-~~~~~~~~~~~~~~a~~~~~~~~~~---~v~~~~~~~~~~~pP~p~~l~~Lq~~a~k~~g~s~~~tl~iaQ~LYE  147 (403)
T PF01131_consen   72 GGFE-FKNDDKKRFDDKEEAEQILEKLKNS---KVTEVEEKEKKKPPPLPFNLSTLQKEASKKLGFSAKETLDIAQKLYE  147 (403)
T ss_dssp             CCS--EETTEES-CTSHHHHHHHHHHHHHC---EEEEEEEEEEEE----SB-HHHHHHHHHHHH---HHHHHHHHHHHHH
T ss_pred             cccc-cccccccccccHHHHHHHhhcccCc---eEEEEEEEEeeecCCChHHHHHHHHHHHHHhhhhHHHHHHHHHHHHh
Confidence            5544 3445678999999999999999873   89999999999999999999999999999999999999999999999


Q ss_pred             c-CceeecCCCCCCCCCcccHHHHHHHhccC-C-chhHHHHHHhhCCCCCCCCCCCCCCCCCCccCCCcc--cCCCCHHH
Q psy8714         326 Q-GYVSYPRTETTQYPENFDLVAVLRQQESS-P-DWGDHVREVLSNGISKPRKGKDVGDHPPITPTKLAT--RTQLDGDA  400 (562)
Q Consensus       326 ~-glISYPRTds~~l~~~~~~~~~l~~l~~~-~-~~~~~~~~~~~~~~~~~~~~~~~~~H~AI~PT~~~~--~~~L~~~e  400 (562)
                      + ||||||||||++||++.++..+++.+... + .+...+......  .++++.++++|||||+||...+  ..+|+++|
T Consensus       148 ~~g~ISYPRTds~~l~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~--~~~~~~~kv~aH~AI~PT~~~~~~~~~Ls~~e  225 (403)
T PF01131_consen  148 KHGLISYPRTDSRYLPEDEDLKEILKYLKKHYGEDYFPEAPNLLKS--PKSKNDSKVTAHHAIIPTGKIPPDLSNLSEDE  225 (403)
T ss_dssp             TTTSBS-SS-S---B-HHHGHHHHHHHHHHHTTGGGS-SS--TTSS--STTC-CCC-SSSS-B-BSSSTTHCGHHCHHHH
T ss_pred             hhheeeeeccchhhhcchhhHHHHHHHHHHhccccccccchhhhhc--ccccCCccccCCCCccccccCccchhhcCHHH
Confidence            7 99999999999999987677777766542 1 122222111110  1112344568999999997654  36799999


Q ss_pred             HHHHHHHHHHHHhhcccCceEEEEEEEEEECCeEEEEEEEEEeecceeeeeccccccc--CCCCCCCCCCeeeeeeeEEe
Q psy8714         401 WRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKN--ESIPDFKPGDLIPIQSVKMV  478 (562)
Q Consensus       401 ~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~v~~~~~~~~--~~Lp~l~~G~~~~~~~~~i~  478 (562)
                      ++||+||+|||||+|||||+|+++++.+.++++.|.++|++++++||+++|+....++  ..||.+++|+.+.+.++.+.
T Consensus       226 ~~vY~LI~rr~la~~~~~~~~~~t~v~~~~~~~~F~~~g~~~~~~Gw~~~~~~~~~~~~~~~lp~l~~g~~~~~~~~~~~  305 (403)
T PF01131_consen  226 RKVYDLIARRFLAAFMPDAKYEKTTVTFEVGGEEFKASGKVIIDPGWKKVYPYEEEEDEEEDLPSLKEGDEIPIEDVEIK  305 (403)
T ss_dssp             HHHHHHHHHHHHHHTS--EEEEEEEEEEEETTEEEEEEEEEEEEHGGGGCS-HCHCCTTSBB-----TTEEEEEEEEEEE
T ss_pred             HHHHHHHHHHHHHHHHHHHheeeEEEEEEecCcEEEEEEeEEEECceeEEEEcccccccccccccccCCcEEeecccchh
Confidence            9999999999999999999999999999999999999999999999999997554432  36999999999999999999


Q ss_pred             eeecCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEcCCCeeecchhHHHHHHhhhccCccCCChhhHHHH
Q psy8714         479 ERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAY  558 (562)
Q Consensus       479 e~~TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~~~k~l~~T~~G~~li~~l~~~~~~l~~p~~Ta~~  558 (562)
                      +++|+||+||||++||++||+.|||||||||+||++|++||||++.+++.|+||++|+.|++.|... +.|++|++||.|
T Consensus       306 e~~TkPP~~~Te~~Ll~~Me~~GIGTpATra~iI~~L~~r~Yi~~~k~~~l~~T~~G~~li~~l~~~-~~l~~p~~Ta~~  384 (403)
T PF01131_consen  306 EKKTKPPKRYTEASLLKAMEKAGIGTPATRASIIEKLIKRGYIERSKGKKLIPTPKGRALIEALPNF-PELISPEMTAQW  384 (403)
T ss_dssp             EEEEESS--EBHHHHHHHHHHTTSS-TTTHHHHHHHHHHTTSEEE-ETTEEEEBHHHHHHHHHHHHC-CCCCSHHHHHHH
T ss_pred             hhccCCCCCCCHHHHHhhhhhcCCCccccHHHHHHHhhccceeecccCceeeeehHHHHHHHHHHhh-HHhcCHHHHHHH
Confidence            9999999999999999999999999999999999999999999985568999999999999998554 789999999999


Q ss_pred             HhhC
Q psy8714         559 RVQA  562 (562)
Q Consensus       559 E~~L  562 (562)
                      |..|
T Consensus       385 E~~L  388 (403)
T PF01131_consen  385 EEKL  388 (403)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            9875

e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. Type IA topoisomerases are comprised of four domains that together form a toroidal structure with a central hole large enough to accommodate single- and double-stranded DNA: an N-terminal alpha/beta Toprim domain, domain 2 and the C-terminal domain 4 are winged-helix domains, and domain 3 is a beta-barrel. Domains 1 (Toprim) and 3 form the active site of the enzyme, while the winged helix domains 2 and 4 form a single-strand DNA-binding groove [, ]. This entry represents the central portion of the enzyme, which covers domains 2 and 3 in topoisomerase type IA enzymes. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome; PDB: 1CYY_A 3PWT_A 1CY4_A 1CY9_A 1ECL_A 1CY7_A 1CY8_A 1CY6_A 1MW8_X 1CY0_A ....

>cd00186 TOP1Ac DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases

Probab=100.00  E-value=5.9e-94  Score=761.40  Aligned_cols=348  Identities=32%  Similarity=0.523  Sum_probs=307.6

Q ss_pred             hHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhhhhhhhhhhcccCcceEEEEEEEeeCCe
Q psy8714         169 FEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNGV  248 (562)
Q Consensus       169 ~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~  248 (562)
                      ++++||.||+++|||||||+||++|+.++.      ++++|+||||||||+|||+||+||+||+|++||.|         
T Consensus         2 ~l~~a~~aR~~~D~liG~n~sr~~t~~~~~------~~~lS~GRVQtPtL~liv~Re~ei~~F~p~~y~~i---------   66 (381)
T cd00186           2 NLVNAQLARRILDRLVGFNLSRLLTKKLRR------KGVLSAGRVQSPTLGLIVEREREIKAFVPEDYWEI---------   66 (381)
T ss_pred             cHHHHHHHHHHHHHHhhhhhhHHHHHHhCC------CCCCccccchhhHhHHHHHHHHHHHhCCCcceEEe---------
Confidence            688999999999999999999999987753      23699999999999999999999999999999998         


Q ss_pred             EEEEEeecccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHHHHHHHHHhhCCCCHHHHHHHHHHhHhcCc
Q psy8714         249 AVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGY  328 (562)
Q Consensus       249 ~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl~iaQ~LYE~gl  328 (562)
                                                 +.++|+++++++++.+||+||||++||++||++|||||++||++||+|||+||
T Consensus        67 ---------------------------~~~~v~~~~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl~iaQ~LYe~gl  119 (381)
T cd00186          67 ---------------------------KEAVVVSVEKKEKKKNPPPPFTTSTLQQEASSKLGFSAKKTMQIAQKLYEAGL  119 (381)
T ss_pred             ---------------------------eeEEEEEEEeeeeecCCCCCcCHHHHHHHHHHhcCCCHHHHHHHHHHHHcCCe
Confidence                                       24789999999999999999999999999999999999999999999999999


Q ss_pred             eeecCCCCCCCCCcc--cHHHHHHHhccCCchhHHHHHHhhCCCCCCCCCCCCCCCCCCccCCCcc----cCCCCHHHHH
Q psy8714         329 VSYPRTETTQYPENF--DLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVGDHPPITPTKLAT----RTQLDGDAWR  402 (562)
Q Consensus       329 ISYPRTds~~l~~~~--~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~H~AI~PT~~~~----~~~L~~~e~~  402 (562)
                      ||||||||++||+++  .+..++..+.....+..  ..... ...+..+.++++|||||+||+..+    ...|+++|++
T Consensus       120 ISYPRTds~~ls~~~~~~~~~~~~~~~~~~~~~~--~~~~~-~~~~~~~~~~~~aH~AI~PT~~~~~~~~~~~l~~~e~~  196 (381)
T cd00186         120 ITYPRTDSTRLSEEAILEAREYIQAIYGKEYLYP--APLLG-RRNPKRGKKEQGAHEAIRPTKVAPTPELEANLSEDEFK  196 (381)
T ss_pred             eeecCCCCccCCHHHHHHHHHHHHHhcCccccch--hhccc-cccccCCCCCcCCCCCCCcCCCCcCchhhccCCHHHHH
Confidence            999999999999986  34555555543221111  11111 111223445568999999998765    3689999999


Q ss_pred             HHHHHHHHHHhhcccCceEEEEEEEEEECCeEEEEEEEEEeecceeeeecccccc-cCCCCCCCCCCeeeeeeeEEeeee
Q psy8714         403 LYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMK-NESIPDFKPGDLIPIQSVKMVERK  481 (562)
Q Consensus       403 vY~lI~rr~la~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~v~~~~~~~-~~~Lp~l~~G~~~~~~~~~i~e~~  481 (562)
                      ||+||+|||||+||+||+|++++|.++++++.|.++|++++++||+.+|+.++.+ +..+|.+++|+.+.+.++.+.+++
T Consensus       197 iY~LI~rrfla~~~~~~~~~~t~v~~~~~~~~F~a~g~~i~~~Gw~~v~~~~~~~~~~~~p~l~~g~~~~~~~~~~~~~~  276 (381)
T cd00186         197 LYELIWRRFLASQMADAKYEETTVTLEIGGEKFKASGKVLLEDGWLEVYPEEKDDEEEEPPPLKEGDELKLEEVELEEKE  276 (381)
T ss_pred             HHHHHHHHHHHHhCchhhEEEEEEEEEECCeEEEEEEEEEeeCCHHHHhCcccccccccCCCCCCCCEEeeeeeeeeecc
Confidence            9999999999999999999999999999999999999999999999999765443 345899999999999999999999


Q ss_pred             cCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEcCCCeeecchhHHHHHHhhhccCccCCChhhHHHHHhh
Q psy8714         482 TTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRVQ  561 (562)
Q Consensus       482 TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~~~k~l~~T~~G~~li~~l~~~~~~l~~p~~Ta~~E~~  561 (562)
                      |+||+||||++||++||+.|||||||||+||++|++||||.. +|+.|+||++|+.|+++|....+.|++|+|||.||.+
T Consensus       277 T~PP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~-~~k~l~pT~~G~~li~~l~~~~~~l~~p~lTa~~E~~  355 (381)
T cd00186         277 TQPPPRYTEASLIKLMEKRGIGRPSTYASIIETLLDRGYVEK-EKKKLIPTELGFAVIELLEKHFPELVDPEFTAKLEEK  355 (381)
T ss_pred             cCCCCCCCHHHHHHHHHhCCCCccccHHHHHHHHHhCCcEEe-eCCEEeECHHHHHHHHHHHHhchhccCHhHHHHHHHH
Confidence            999999999999999999999999999999999999999997 6779999999999999998777789999999999987


Q ss_pred             C
Q psy8714         562 A  562 (562)
Q Consensus       562 L  562 (562)
                      |
T Consensus       356 L  356 (381)
T cd00186         356 L  356 (381)
T ss_pred             H
Confidence            6

Topoisomerases clevage single or double stranded DNA and then rejoin the broken phosphodiester backbone. Proposed catalytic mechanism of single stranded DNA cleavage is by phosphoryl transfer through a tyrosine nucleophile using acid/base catalysis. Tyr is activated by a nearby group (not yet identified) acting as a general base for nucleophilic attack on the 5' phosphate of the scissile bond. Arg and Lys stabilize the pentavalent transition state. Glu then acts as a proton donor for the leaving 3'-oxygen, upon cleavage of the scissile strand.

>PRK14701 reverse gyrase; Provisional

Probab=100.00  E-value=3.4e-91  Score=833.84  Aligned_cols=289  Identities=19%  Similarity=0.234  Sum_probs=233.0

Q ss_pred             eEEEEecccCcCCcchHHhhcccccCCCCc-----eeeeeeeeEcCCCcEEEEEEecccccccccccCCCCCccCC----
Q psy8714           6 KKLVPASEIKLARPSLISLLTPLQRMNGAC-----SVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVD----   76 (562)
Q Consensus         6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~~~-----~~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~~~~y~~W~~~~----   76 (562)
                      +.||||||     |++|+.||.++|....-     ++|++    .++++.++||||.|||++|..|++|..|...+    
T Consensus       581 ~~LiIaEk-----Ps~Ak~IA~~lg~~~~r~~g~~~~ye~----~~g~~~~~Vtas~GHl~dL~~~~~~~g~~~~~~~f~  651 (1638)
T PRK14701        581 SALMIVES-----PNKARTIANFFGQPSVRKIGDLVAYEV----SIGDHMLIITASGGHVFDLVTNEGFHGVLINNNLFI  651 (1638)
T ss_pred             CeEEEEeC-----hHHHHHHHHHhCCCccccCCCcceEEE----ecCCcEEEEEEecceeccCCCccccCccccccCccC
Confidence            67999999     99999999999864321     22222    12334689999999999998776665554322    


Q ss_pred             C-----------CCCCCC-------Ccc-cccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhccc
Q psy8714          77 P-----------LELFSC-------PTE-KREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQINI  137 (562)
Q Consensus        77 p-----------~~~~~~-------~~~-~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~  137 (562)
                      |           ..+|..       |.. ........++++.|++++++||+||||||||||||+|||+|++++..    
T Consensus       652 P~y~~~k~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~lr~l~~~ad~viiatD~DrEGE~I~~~i~~~~~~----  727 (1638)
T PRK14701        652 PIYDSIKRCRDCGHQFTDWEDKGVCPRCGSKNVDDAKENIKAMRELAHEVDEILIGTDPDTEGEKIAWDIRNVLAP----  727 (1638)
T ss_pred             CcccccccCCCchhhccccccccccccccccccccHHHHHHHHHHHHHhCCeEEECCCCChhhHHHHHHHHHHhcc----
Confidence            1           112211       000 00112234578889999999999999999999999999999999853    


Q ss_pred             CCCCcEEEEEecccCHHHHHHHHHhCCCChHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccc
Q psy8714         138 NSPKTVWRARFSAITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPT  217 (562)
Q Consensus       138 ~~~~~v~Rl~~sslt~~~I~~A~~nl~~~~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTpt  217 (562)
                       ++++++|+|||++|+++|++||+||+++|.+++.||.||+++||+||||+||++|..+++       ..+|+|||||||
T Consensus       728 -~~~~i~R~~fs~lT~~aI~~A~~nlr~~d~~l~~A~~aRr~~D~~iG~nlSr~l~~~~~~-------~~lS~GRVQTPt  799 (1638)
T PRK14701        728 -YGPNIKRIEFHEVTRRAILKAIKEARDIDENRVKAQIVRRIEDRWIGFELSQKLWEVFED-------RNLSAGRVQTPV  799 (1638)
T ss_pred             -CCCCeeEEEEccCCHHHHHHHHhCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHhccC-------Cceeecccccch
Confidence             368999999999999999999999999999999999999999999999999999976542       359999999999


Q ss_pred             hhhhhhhhhhhhcccCcceEEEEEEEeeCCeEEEEEeecccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCC
Q psy8714         218 LGFCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALN  297 (562)
Q Consensus       218 L~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~  297 (562)
                      |+|||+|++||+| +|++||.+...+   +  +.+.|..    +++           ...+.|.+++.++++.+||+|||
T Consensus       800 L~~Iv~Re~ei~~-~~~~~~~i~~~~---~--~~~~~~~----~~~-----------~~~~~V~~v~~k~~~~~pP~pf~  858 (1638)
T PRK14701        800 LGWIIQRYKEFTE-SKVPFLGIILEN---D--LTVTIED----SKD-----------EVEVEVELVEEEEKERNPLPPYT  858 (1638)
T ss_pred             hhhhHhhHHHHhc-CCCceEEEEEcC---c--eEEEecc----ccc-----------CCeEEEEEEEeeEEEccCCCCcC
Confidence            9999999999999 599999986543   2  3333321    111           02478999999999999999999


Q ss_pred             HHHHHHHHHhhCCCCHHHHHHHHHHhHhcCceeecCCCC
Q psy8714         298 TVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTET  336 (562)
Q Consensus       298 l~~Lq~~a~~~~g~s~~~tl~iaQ~LYE~glISYPRTds  336 (562)
                      |++||++||++|||||++||++||+|||+|++|||||..
T Consensus       859 t~~Lq~~As~~~g~s~~~tm~iAQ~LYE~g~~~~p~t~V  897 (1638)
T PRK14701        859 TDTMLRDASAFLKLSAKETMKLAQDLFEAGLCVTPDTYV  897 (1638)
T ss_pred             HHHHHHHHHHhcCCCHHHHHHHHHHHHhCceeeCCCcee
Confidence            999999999999999999999999999999999999975

>COG1110 Reverse gyrase [DNA replication, recombination, and repair]

Probab=100.00  E-value=1.1e-77  Score=662.04  Aligned_cols=499  Identities=23%  Similarity=0.333  Sum_probs=390.8

Q ss_pred             EEEEecccCcCCcchHHhhcccccCCCCc-----eeeeeeeeEcCCCcEEEEEEecccccccccccCCC-------CCcc
Q psy8714           7 KLVPASEIKLARPSLISLLTPLQRMNGAC-----SVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYN-------NWDK   74 (562)
Q Consensus         7 ~l~~ae~~~~~~p~~a~~~~~~~g~~~~~-----~~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~~~~y~-------~W~~   74 (562)
                      .|+|+|+     |..|++||..+|.....     .+|+-   .-|+. ...||++.||+++|-..+.+-       +|-.
T Consensus       619 ~L~IVES-----PnKARTIA~FFgrPS~R~~~~~~vYEv---~~gD~-vL~ItAS~GHv~DLvt~~g~hGvl~~~~~~vP  689 (1187)
T COG1110         619 ALMIVES-----PNKARTIASFFGRPSVRRLGGGVVYEV---AIGDL-VLTITASGGHVFDLVTEPGVHGVLVKDGKYVP  689 (1187)
T ss_pred             eEEEEeC-----ChHHHHHHHHhCCcceeeeCCeeEEEE---ecCCe-EEEEEecCCeeEEeecccccceeeccCCceEe
Confidence            4899999     88999999999974332     22221   12544 467999999999994322220       1111


Q ss_pred             -------CC-CCCCC-----CCCcccc-cCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCC
Q psy8714          75 -------VD-PLELF-----SCPTEKR-EATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSP  140 (562)
Q Consensus        75 -------~~-p~~~~-----~~~~~~~-~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~  140 (562)
                             |. -...|     .+|.... ...++..+|+.|++++-.+|+|+||||||.|||-|||+|..++.+     ++
T Consensus       690 vY~tIKrC~dcg~q~~~~~~~cP~Cgs~~v~d~~~~ve~lRelA~EvDeVlIgTDPDtEGEKIawDv~~~l~P-----y~  764 (1187)
T COG1110         690 VYDTIKRCRDCGEQFVDSEDKCPRCGSRNVEDKTETVEALRELALEVDEILIGTDPDTEGEKIAWDVFNYLRP-----YN  764 (1187)
T ss_pred             hHHHHHHHhhcCceeccccccCCCCCCccccccHHHHHHHHHHHhhcCEEEEcCCCCCccchhHHHHHHhhCc-----CC
Confidence                   11 00011     1333221 123456789999999999999999999999999999999999975     47


Q ss_pred             CcEEEEEecccCHHHHHHHHHhCCCChHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhh
Q psy8714         141 KTVWRARFSAITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGF  220 (562)
Q Consensus       141 ~~v~Rl~~sslt~~~I~~A~~nl~~~~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~l  220 (562)
                      ..|+|+.||++|+.+|.+|++|+++.|.|++.||..|++.|++|||.||+.++..+.       +.-+|+||||||+|++
T Consensus       765 ~nikR~eFHEVTrrAIleAl~n~r~vd~nlVkAQiVRRIeDRWIGF~LS~~Lw~~F~-------~~nLsAGRVQTPVLGW  837 (1187)
T COG1110         765 PNVKRIEFHEVTRRAILEALKNPRDVDENLVKAQIVRRIEDRWIGFELSQKLWDVFN-------NKNLSAGRVQTPVLGW  837 (1187)
T ss_pred             CceeEEEeeeecHHHHHHHHhCccccchhhhHHHhhhhhhhcccceeecHHHHHHhC-------ccCcccccccccccee
Confidence            889999999999999999999999999999999999999999999999998776553       2359999999999999


Q ss_pred             hhhhhhhhhcccCcceEEEEEEEeeCCeEEEEEeecccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHHH
Q psy8714         221 CVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVE  300 (562)
Q Consensus       221 Iv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~  300 (562)
                      ||+|+++-+.-+.  |..+..       .+..     .+-+...++.+...+.. ....|.++..++...+||+||+|.+
T Consensus       838 IV~Ry~e~~~~~~--~~~~~~-------~~~~-----~~~~~~~~~~~~~~~~~-~~v~v~~~~e~ee~~~PlPPyTTDt  902 (1187)
T COG1110         838 IVNRYEEYKEKRG--YLVIQL-------DLDL-----PSGNREEVENVKRKLKL-IVVEVVDVVEREEEKNPLPPYTTDT  902 (1187)
T ss_pred             ehhhHHHHhhccc--eeEeec-------ccee-----eccchhhhhhhhhhccc-ceEEEeehhhhhhccCCCCCcCcch
Confidence            9999998876444  443311       1111     22344555655555443 3466777666677789999999999


Q ss_pred             HHHHHHhhCCCCHHHHHHHHHHhHhcCceeecCCCCCCCCCcc-c-HHHHHHHhccCCchhHHHHHHhhCCCCCCCCCCC
Q psy8714         301 LMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENF-D-LVAVLRQQESSPDWGDHVREVLSNGISKPRKGKD  378 (562)
Q Consensus       301 Lq~~a~~~~g~s~~~tl~iaQ~LYE~glISYPRTds~~l~~~~-~-~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~  378 (562)
                      ++.+||++||+|+++||++||.|+|.|+|||+||||+++|..- . ..+.|..             -+......||.|..
T Consensus       903 ~L~dAs~~L~lsa~~~M~iaQdLFE~GlITYHRTDSTrVS~~Gi~vAreyl~~-------------~~~e~~f~pR~Wge  969 (1187)
T COG1110         903 MLRDASRRLRLSADETMQIAQDLFEGGLITYHRTDSTRVSDVGIRVAREYLRK-------------EFGEEYFRPRSWGE  969 (1187)
T ss_pred             HHHHHHHHhCCChhHHHHHHHHHHhccceEEeecCCcccchhhHHHHHHHHHH-------------hhccccccCCcccc
Confidence            9999999999999999999999999999999999999999742 1 1222211             11223468999988


Q ss_pred             CCCCCCCccCCCcc---------------cCCCCHHHHHHHHHHHHHHHhhcccCceEEEEEEEEEECCeEEEEEE-EEE
Q psy8714         379 VGDHPPITPTKLAT---------------RTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEA-KYL  442 (562)
Q Consensus       379 ~~~H~AI~PT~~~~---------------~~~L~~~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~~~F~a~g-~~~  442 (562)
                      .+||+||+||...+               +..|+.++.+||+||.|||+|+||+|+++....+.+..++..-...+ ..+
T Consensus       970 ~GAHEaIRPtrPid~~eL~~~i~~G~i~~~~~Lt~~HlrvYdLIFrRFmASQm~pa~v~~~~~~i~~~~~~~~~e~~ve~ 1049 (1187)
T COG1110         970 EGAHEAIRPTRPIDVEELITLIEEGVIQLPIRLTKNHLRVYDLIFRRFMASQMRPAKVLKEKAEVKADGKDVELEALVEI 1049 (1187)
T ss_pred             CCcccccCCCCCCCHHHHHHHHHcCCeeccchhhHHHHHHHHHHHHHHHHhhCCceeEEEEEEEEecCcceeeeeehhhh
Confidence            89999999998643               13489999999999999999999999999999999999875544444 445


Q ss_pred             eecceeeeecccccccCCCCCCCCCCeeeeeeeEEeeeecCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEE
Q psy8714         443 LHPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVT  522 (562)
Q Consensus       443 ~~~Gw~~v~~~~~~~~~~Lp~l~~G~~~~~~~~~i~e~~TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~  522 (562)
                      ...||..+|+.     ..+|.+..|+ +.+....+......  ..||++++++.|++.|||+|||||.||++|.+||||.
T Consensus      1050 ~~~G~~~vy~~-----~~~p~l~~g~-l~v~~~~~~~~~kv--~lytqg~vi~~MKerGIGRPSTYAkive~L~~RgYvi 1121 (1187)
T COG1110        1050 LEDGFALVYPT-----RVLPELEKGT-LKVTEVEIRKVSKV--YLYTQGEVVEEMKERGIGRPSTYAKIVETLLRRGYVI 1121 (1187)
T ss_pred             hccchhhhccc-----cccCccCCCc-eeeeeeEEEEcccc--cccccchHHHHHHhcCCCCCcHHHHHHHHHhcCCeEE
Confidence            68999999862     3478889998 77766665544433  4799999999999999999999999999999999998


Q ss_pred             EcCCCe-eecchhHHHHHHhhhccCccCCChhhHHHHHhhC
Q psy8714         523 VTSGRR-LVPTSLGIVLVHGYQKIDRELVEPTMRSAYRVQA  562 (562)
Q Consensus       523 ~~~~k~-l~~T~~G~~li~~l~~~~~~l~~p~~Ta~~E~~L  562 (562)
                      -.+|++ ++||.+|+.+++.|..-.+.++|.+.|..+|+.|
T Consensus      1122 e~kg~~~lipTk~Gi~Vy~yL~~~~~~lVSEerTR~LEe~M 1162 (1187)
T COG1110        1122 ESKGRKKLIPTKLGIEVYEYLSEKYKKLVSEERTRRLEEIM 1162 (1187)
T ss_pred             EecCceEeccccccHHHHHHHHHhcccccchhHHHHHHHHH
Confidence            756654 9999999999999988789999999999999864

>KOG1957|consensus

Probab=100.00  E-value=4.1e-74  Score=584.70  Aligned_cols=485  Identities=54%  Similarity=0.845  Sum_probs=438.7

Q ss_pred             EEEecccCcCCcchHHhhcccccC------CCCceeeeeeeeEcCCCcEEEEEEecccccccccccCCCCCccCCCCCCC
Q psy8714           8 LVPASEIKLARPSLISLLTPLQRM------NGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELF   81 (562)
Q Consensus         8 l~~ae~~~~~~p~~a~~~~~~~g~------~~~~~~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~~~~y~~W~~~~p~~~~   81 (562)
                      |.+|||     ||+|..||.+++.      .+.+++.+|+|.|.|....|.||++.||+|.||||++|++|...||.+||
T Consensus         5 lmvaek-----psla~sia~ils~g~~s~~kg~csvhe~~g~f~g~~~~fk~tsvcghvmsldf~~kyn~w~~vdp~elf   79 (555)
T KOG1957|consen    5 LMVAEK-----PSLADSIANILSNGQASKRKGWCSVHEYDGQFRGRAARFKVTSVCGHVMSLDFPPKYNNWDKVDPAELF   79 (555)
T ss_pred             eEeecC-----chHHHHHHHHhhCCccccccCceeeeeccccccCceeeEEEeeeeceeEeccCchhcCCccccCHHHHh
Confidence            779999     9999998877643      34588999999999999999999999999999999999999999999999


Q ss_pred             CCCcccccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHHHHH
Q psy8714          82 SCPTEKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMW  161 (562)
Q Consensus        82 ~~~~~~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~A~~  161 (562)
                      ..|..+++++++.++.+.|..+++.||.+|+|.|||+|||+|.+||++..+.+|+.. ...++|+.||++|+++|.+|+.
T Consensus        80 ~apt~kkeanpk~~m~kfl~~eargcdy~vlwldcdkegenicfevidav~~~m~~~-~~~tyra~fsaitekdi~~am~  158 (555)
T KOG1957|consen   80 SAPTEKKEANPKMNMNKFLASEARGCDYLVLWLDCDKEGENICFEVIDAVKCVMNRS-DFKTYRAHFSAITEKDIKKAMR  158 (555)
T ss_pred             CCcchhcccCchhhHHHHHhhhccCCcEEEEEeecCCCcCeeehhhhhhhhhhhccC-cceEEeeeeccccHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999998888633 4567999999999999999999


Q ss_pred             hCCCChHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhhhhhhhhhhcccCcceEEEEE
Q psy8714         162 NLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDL  241 (562)
Q Consensus       162 nl~~~~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lIv~Re~eI~~F~p~~y~~i~~  241 (562)
                      ||..+|.|.+.+..|||++|..|         +         .+..+|+|.||||||++.|+|...|+.|+|+.||.++.
T Consensus       159 ~lg~p~~nea~svdarqeldlri---------l---------ds~~isygpcqtptlgfcv~rhd~i~tfkpe~~w~l~~  220 (555)
T KOG1957|consen  159 NLGEPDQNEALSVDARQELDLRI---------L---------DSSLISYGPCQTPTLGFCVTRHDQIQTFKPEQYWVLQT  220 (555)
T ss_pred             hcCCCCcchhcccchhhhhhhhh---------h---------hhcceeecCCCCCcceeeeeehhhhhccCccceEEEee
Confidence            99999999999999999999987         1         13579999999999999999999999999999999999


Q ss_pred             EEeeCCeEEEEEeecccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHHHHHHHHHhhCCCCHHHHHHHHH
Q psy8714         242 TLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAE  321 (562)
Q Consensus       242 ~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl~iaQ  321 (562)
                      .+..++  +...|+++|++|.+.|.-+++.++..+++.|.+|.+|+..+..|..+||.+|.+-|                
T Consensus       221 ~~~~~~--~~lew~r~rvfd~eia~~f~~~vk~~~~a~v~~vs~ke~~k~rp~alntvel~rv~----------------  282 (555)
T KOG1957|consen  221 NFTTDD--LSLEWQRGRVFDAEIARVFLNRVKECKTALVEDVSKKEARKERPCALNTVELMRVA----------------  282 (555)
T ss_pred             ecCCCC--ccchhhhcchhhHHHHHHHHHHHHhhhhheehhhhhhHHhhcCCcccchhheeeee----------------
Confidence            987665  88999999999999999999999988999999999999999999999999998877                


Q ss_pred             HhHhcCceeecCCCCCCCCCcccHHHHHHHhccCCchhHHHHHHhhCCCCCCCCCCCCCCCCCCccCCCcccCCCCHHHH
Q psy8714         322 RLYTQGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVGDHPPITPTKLATRTQLDGDAW  401 (562)
Q Consensus       322 ~LYE~glISYPRTds~~l~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~H~AI~PT~~~~~~~L~~~e~  401 (562)
                                 +|+++.+|+++|-        +..         +.+++..++.+.++++|++|.|-+.......+.+-+
T Consensus       283 -----------itett~y~~nfd~--------si~---------~~D~L~~~s~gtdAgdgpPitpmr~~~R~m~~~dtk  334 (555)
T KOG1957|consen  283 -----------ITETTAYPANFDT--------SII---------LGDTLFEASFGTDAGDGPPITPMRKCNRYMKSGDTK  334 (555)
T ss_pred             -----------EeecccCcccccc--------ccc---------cccccccccccCcCCCCCCcCcccccccccccccce
Confidence                       4999999998851        110         112345566777788999999998766666777889


Q ss_pred             HHHHHHHHHHHhhcccCceEEEEEEEEEECCeEEE--EEEEEEeecceeeeecccc-------cccCCCCCCCC------
Q psy8714         402 RLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFT--MEAKYLLHPGFTGVMTWSA-------MKNESIPDFKP------  466 (562)
Q Consensus       402 ~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~~~F~--a~g~~~~~~Gw~~v~~~~~-------~~~~~Lp~l~~------  466 (562)
                      +||..++++|++.-+.+.+|..+++...++++.|.  ..|+++.+.|+..+.....       -++...|+.+.      
T Consensus       335 RLY~~vCqhf~~tp~~~~~k~it~~k~slgdeqf~lw~~Gk~~~~~gft~fm~n~p~m~wgagcdECthPScq~slSmlg  414 (555)
T KOG1957|consen  335 RLYCYVCQHFYATPQFKCKKVITTVKCSLGDEQFILWCTGKRLREFGFTPFMPNNPKMPWGAGCDECTHPSCQQSLSMLG  414 (555)
T ss_pred             eecchhhhhheeccCcCceEEEeeeeeccCCeeEEeccCcceeccCCccccccCCCccccccCCCccCCchHHhhhhccc
Confidence            99999999999999999999999999999999999  9999999999999975211       12455666555      


Q ss_pred             -CCeeeeeeeEEeeeecCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEcCCCeeecchhHHHHHHhhhcc
Q psy8714         467 -GDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKI  545 (562)
Q Consensus       467 -G~~~~~~~~~i~e~~TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~~~k~l~~T~~G~~li~~l~~~  545 (562)
                       |+.+.+.++.+.+..|.||-++|+..++..|+++||||.|.-+-+|..+-+|+|+.++.|+.+.||++|+.++.++..+
T Consensus       415 iG~~vEc~~v~Lv~~qTsPkwylTcnkcisvme~hgigtdasI~VhinsiceRnYv~Ve~gr~~~Pt~Lg~~l~~Gy~~~  494 (555)
T KOG1957|consen  415 IGQCVECESVELVLDQTSPKWYLTCNKCISVMEKHGIGTDASIPVHINSICERNYVTVESGRALVPTPLGETLVRGYVKC  494 (555)
T ss_pred             ceeEEEeccEEEEecCCCCCceeehhhhHHHHHhhcccceeeEEEeecchhhhheEeeecCcccCCCccchhhhcCceee
Confidence             9999999999999999999999999999999999999999999999999999999998999999999999999999989


Q ss_pred             CccCCChhhHHHHHhhC
Q psy8714         546 DRELVEPTMRSAYRVQA  562 (562)
Q Consensus       546 ~~~l~~p~~Ta~~E~~L  562 (562)
                      +|++.-|.+.+..|.+|
T Consensus       495 DP~l~lpt~r~~~es~~  511 (555)
T KOG1957|consen  495 DPELVLPTMRKEAESQL  511 (555)
T ss_pred             CcceechhHHHHHHhhc
Confidence            99999999999999764

>smart00437 TOP1Ac Bacterial DNA topoisomerase I DNA-binding domain

Probab=100.00  E-value=4.4e-68  Score=534.09  Aligned_cols=250  Identities=32%  Similarity=0.538  Sum_probs=216.8

Q ss_pred             cceeeccCCCCCCHHHHHHHHHhhCCCCHHHHHHHHHHhHhcCceeecCCCCCCCCCcc--cHHHHHHHhccCCchhHHH
Q psy8714         285 SSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENF--DLVAVLRQQESSPDWGDHV  362 (562)
Q Consensus       285 ~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl~iaQ~LYE~glISYPRTds~~l~~~~--~~~~~l~~l~~~~~~~~~~  362 (562)
                      +++++.+||+||||++||++||++|||||++||++||+|||+|+||||||||+|||+++  ++..++..+.. +.|...+
T Consensus         2 ~~~~~~~pP~pf~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYe~g~iTYPRTds~~l~~~~~~~~~~~l~~~~~-~~~~~~~   80 (259)
T smart00437        2 EKEKKKNPPPPFTTSTLQQEASRKLGFSAKKTMQIAQKLYEKGLITYPRTDSTRLSEEAVLEARNYISKHYG-KEYLPLA   80 (259)
T ss_pred             CCcccCCCCCCccHHHHHHHHHHhcCCCHHHHHHHHHHHHhCCeeEecCCCCCcCCHHHHHHHHHHHHHhhc-hhhhhhh
Confidence            46688999999999999999999999999999999999999999999999999999986  35566666543 2343322


Q ss_pred             HHHhhCCCCCCC-CCCCCCCCCCCccCCCccc----CCCCHHHHHHHHHHHHHHHhhcccCceEEEEEEEEEECCeEEEE
Q psy8714         363 REVLSNGISKPR-KGKDVGDHPPITPTKLATR----TQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTM  437 (562)
Q Consensus       363 ~~~~~~~~~~~~-~~~~~~~H~AI~PT~~~~~----~~L~~~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~~~F~a  437 (562)
                      .....  ...+. +.++++||||||||...+.    .+|+++|++||+||+|||||+|||||+|++++|.+.++++.|.+
T Consensus        81 ~~~~~--~~~~~~~~~k~~~H~aI~PT~~~~~~~~~~~L~~~e~~iY~lI~rr~la~~~~~~~~~~t~v~~~~~~~~F~a  158 (259)
T smart00437       81 VSLLK--PRKPRWGKKEQGAHEAIRPTKPIPTPELEKELSEDEKKLYELIWRRFLASQMPDAKYEETKVIIKIGGEKFKA  158 (259)
T ss_pred             hhhcc--CccccCCCCCCCCCCCCCccCCCCCchhhhhCCHHHHHHHHHHHHHHHHHhChhheEEEEEEEEEECCeEEEE
Confidence            11111  11222 3345689999999987542    47999999999999999999999999999999999999999999


Q ss_pred             EEEEEeecceeeeecccccc-cCCCCCCCCCCeeeeeeeEEeeeecCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhh
Q psy8714         438 EAKYLLHPGFTGVMTWSAMK-NESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNIC  516 (562)
Q Consensus       438 ~g~~~~~~Gw~~v~~~~~~~-~~~Lp~l~~G~~~~~~~~~i~e~~TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~  516 (562)
                      +|++++++||+.||++++.+ +..||.+++|+.+.+.++.+.+++|+||+||||++||++||+.|||||||||+||++|+
T Consensus       159 ~g~~i~~~Gw~~v~~~~~~~~~~~lp~~~~g~~~~~~~~~~~e~~TkPP~~~Te~tLl~~Me~~GIGTpATra~iIe~L~  238 (259)
T smart00437      159 KGKTLLFDGWLKVYPEEKKEEEIELPTLKKGDELKVEEVEVEEKKTKPPARYTEASLIKLMEKRGIGRPSTYAEIIETLL  238 (259)
T ss_pred             EEEEEeECCHHHhhcccccCccccCCCcCCCCEeeeeeeEEEecccCCCCCCCHHHHHHHHHHCCCCchhhHHHHHHHHH
Confidence            99999999999999765443 35699999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCeEEEcCCCeeecchhHHHH
Q psy8714         517 QRNYVTVTSGRRLVPTSLGIVL  538 (562)
Q Consensus       517 ~r~Yi~~~~~k~l~~T~~G~~l  538 (562)
                      +||||.+ +|+.|+||++|+.|
T Consensus       239 ~r~Yi~~-~~k~l~~T~~G~~l  259 (259)
T smart00437      239 DRGYVTK-EKKKLIPTELGIAV  259 (259)
T ss_pred             hCCcEEe-eCCEEeEccceecC
Confidence            9999997 67899999999864

Bacterial DNA topoisomerase I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase alpha subunit

>cd03362 TOPRIM_TopoIA_TopoIII TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III

Probab=100.00  E-value=1.8e-33  Score=261.71  Aligned_cols=147  Identities=33%  Similarity=0.400  Sum_probs=114.7

Q ss_pred             eEEEEecccCcCCcchHHhhcccccCCCCceee--eeeeeEcCCCcEEEEEEecccccccccccCCCCCccCCCCC--CC
Q psy8714           6 KKLVPASEIKLARPSLISLLTPLQRMNGACSVH--EWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLE--LF   81 (562)
Q Consensus         6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~~~~~~--~~~g~~~g~~~~~~Vt~~~GHl~~l~~~~~y~~W~~~~p~~--~~   81 (562)
                      |.||||||     ||+|+.||+++|....-...  .+.++++|.  .|+||||.|||++|++|++|..|....+..  ++
T Consensus         1 ~~LiIAEK-----Ps~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~--~~~vt~~~GHl~~l~~p~~y~~~~~~~~~~~p~~   73 (151)
T cd03362           1 MVLIIAEK-----PSVAKAIAKILGGGSKKKGKGRYYEFYGEGG--GYVVTWASGHLLELDFPEEYDPWDKVWPLEDPLF   73 (151)
T ss_pred             CEEEEecC-----HHHHHHHHHHhCCCCccCCcccccceecCCC--CEEEEEEhhHhhcccChHHhccCCCCCccccCCc
Confidence            68999999     99999999999765432111  134466665  489999999999999999998776544322  33


Q ss_pred             CCCcccccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHHHHH
Q psy8714          82 SCPTEKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMW  161 (562)
Q Consensus        82 ~~~~~~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~A~~  161 (562)
                      +............++++.|++++++||+||||||||||||+|||+|+++++..    .+++++|+|||++|+++|++||+
T Consensus        74 ~~~~~~~~~~~~~~~~~~ik~l~~~ad~ii~atD~DrEGE~I~~~i~~~~~~~----~~~~v~R~~fsslT~~~I~~A~~  149 (151)
T cd03362          74 PAPFKLKVDKGKKKQFKVLKKLAKRADEIVIATDADREGELIGREILEYAKCV----KRKPVKRAWFSSLTPKAIRRAFK  149 (151)
T ss_pred             CCceEEEECccHHHHHHHHHHHHhCCCeEEEccCCCccccHHHHHHHHHhCCC----CCCcEEEEEEccCCHHHHHHHHh
Confidence            32222222233456888899999999999999999999999999999999531    26899999999999999999999


Q ss_pred             hC
Q psy8714         162 NL  163 (562)
Q Consensus       162 nl  163 (562)
                      ||
T Consensus       150 nl  151 (151)
T cd03362         150 NL  151 (151)
T ss_pred             cC
Confidence            86

Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.

>cd01028 TOPRIM_TopoIA TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IA family of DNA topoisomerases (TopoIA)

Probab=100.00  E-value=7.3e-33  Score=255.07  Aligned_cols=142  Identities=34%  Similarity=0.401  Sum_probs=111.9

Q ss_pred             eEEEEecccCcCCcchHHhhcccccCCCCceeeeeeeeEcCCCcEEEEEEecccccccccccCCCCCccCCCCCCCCCCc
Q psy8714           6 KKLVPASEIKLARPSLISLLTPLQRMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPT   85 (562)
Q Consensus         6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~~~~~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~~~~y~~W~~~~p~~~~~~~~   85 (562)
                      |.||||||     ||+|+.|++++|..+...    .++++|.  .|+||||.|||++|++|++|..|....+..+++...
T Consensus         1 ~~LiIaEK-----Ps~a~~ia~~L~~~~~~~----~~~~~~~--~~~v~~~~GHl~~l~~~~~~~~~~~~~~~~~~~~~~   69 (142)
T cd01028           1 KVLIIAEK-----PSKAKTIAKILGKGSKKK----GFYGEGG--GYVVTASVGHLLELPFPEEYVDWDKDWPLELFPFEP   69 (142)
T ss_pred             CEEEEEeC-----HHHHHHHHHHhCCCcccC----CceecCC--CEEEEEEccccccCCCcccccccccCCchhhCCCCc
Confidence            68999999     999999999998765421    1466665  489999999999999999998765433322222111


Q ss_pred             ccccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHHHHHhC
Q psy8714          86 EKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNL  163 (562)
Q Consensus        86 ~~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~A~~nl  163 (562)
                      .........++++.|++++++||+||||||||||||+|||+|+++++.     .+++++|+|||++|+++|++||+||
T Consensus        70 ~~~~~~~~~~~~~~ik~l~~~~d~iiiAtD~DrEGE~I~~~i~~~~~~-----~~~~v~R~~fsslT~~~I~~A~~nl  142 (142)
T cd01028          70 KYVVIPDKKKQLKALKKLAKKADEIVLATDPDREGELIAWEILEVLKC-----DNKPVKRAWFSEITPKAIREAFKNL  142 (142)
T ss_pred             eEEeCCcHHHHHHHHHHHHhcCCEEEEcCCCCcchHHHHHHHHHHhCC-----CCCCeEEEEEccCCHHHHHHHHhCc
Confidence            112223344678888888899999999999999999999999999953     1689999999999999999999986

This subgroup contains proteins similar to the Type I DNA topoisomerases: E. coli topisomerases I and III, eukaryotic topoisomerase III and, ATP-dependent reverse gyrase found in archaea and thermophilic bacteria. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA. These enzymes cleave one strand of the DNA duplex, covalently link to the 5' phosphoryl end of the DNA break and allow the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general b

>smart00436 TOP1Bc Bacterial DNA topoisomeraes I ATP-binding domain

Probab=99.97  E-value=1.6e-32  Score=231.01  Aligned_cols=89  Identities=39%  Similarity=0.558  Sum_probs=84.0

Q ss_pred             EEEEEecccCHHHHHHHHHhCCCChHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhhh
Q psy8714         143 VWRARFSAITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCV  222 (562)
Q Consensus       143 v~Rl~~sslt~~~I~~A~~nl~~~~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lIv  222 (562)
                      |+|+|||++|+++|++||+|+++.+.++++||+||+++||++|||+||++|+.++.       +.+|+||||||||+|||
T Consensus         1 v~R~~fs~lt~~~I~~a~~~l~~~~~~l~~a~~aR~~~D~l~G~n~Sr~~t~~~~~-------~~ls~GRVQtptL~lIv   73 (89)
T smart00436        1 IKRIEFSEITKKAIREALKNPREIDENLVNAQLARRILDRLIGFNLSRLLTKKLRK-------GVLSAGRVQTPTLGLIV   73 (89)
T ss_pred             CEEEEEecCCHHHHHHHHHCcccccHHHHHHHHHHHHHHHHHhHhhhHHHHHHhCC-------CCcceecchHHHHHHHH
Confidence            58999999999999999999999889999999999999999999999999987653       36999999999999999


Q ss_pred             hhhhhhhcccCcceEE
Q psy8714         223 ERHDKIRTFKPEPYWL  238 (562)
Q Consensus       223 ~Re~eI~~F~p~~y~~  238 (562)
                      +||+||+||+|++||.
T Consensus        74 ~R~~ei~~F~~~~y~~   89 (89)
T smart00436       74 EREREIKNFVPKPYWE   89 (89)
T ss_pred             HHHHHHHcCCCCCCCC
Confidence            9999999999999994

Extension of TOPRIM in Bacterial DNA topoisomeraes I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase beta subunit

>cd03361 TOPRIM_TopoIA_RevGyr TopoIA_RevGyr : The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to the ATP-dependent reverse gyrase found in archaea and thermophilic bacteria

Probab=99.96  E-value=3.5e-29  Score=236.82  Aligned_cols=143  Identities=23%  Similarity=0.249  Sum_probs=108.3

Q ss_pred             EEEEecccCcCCcchHHhhcccccCC-----CCceeeeeeeeEcCCCcEEEEEEecccccccccccCCCCCccC------
Q psy8714           7 KLVPASEIKLARPSLISLLTPLQRMN-----GACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKV------   75 (562)
Q Consensus         7 ~l~~ae~~~~~~p~~a~~~~~~~g~~-----~~~~~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~~~~y~~W~~~------   75 (562)
                      .||||||     ||+|+.||+++|..     +++++|+|.    +++..|+|||+.|||++|++|+.|..|...      
T Consensus         2 ~LiIaEK-----Ps~Ak~Ia~~L~~~~~~~~~~~~~~e~~----~~~~~~~Vt~~~GHl~~l~~~~~~~~~~~~~~~~~p   72 (170)
T cd03361           2 ALMIVES-----PNKARTIANFFGRPSVRRLGGLVVYEVS----TGDGVLMITASGGHVYDLVTKEGGHGVVEDDGRYVP   72 (170)
T ss_pred             eEEEEeC-----hHHHHHHHHHhCCCcccccCCceeEEEe----cCCeEEEEEeCCCeeecCCCccCccCccccCCccee
Confidence            6999999     99999999999843     234445543    234467899999999999988877653321      


Q ss_pred             --------CCC-CCCC-----CCccc-ccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCC
Q psy8714          76 --------DPL-ELFS-----CPTEK-REATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSP  140 (562)
Q Consensus        76 --------~p~-~~~~-----~~~~~-~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~  140 (562)
                              .|- .+|.     +|... .....+.++++.|++++++||+||+|||||||||+|+|+|+++++..     +
T Consensus        73 ~~~~~~~c~pc~~lF~~~~~~cp~c~~~~~~~~~~~~~~l~~l~~~~~~iiiatD~drEGe~I~~~i~~~~~~~-----~  147 (170)
T cd03361          73 VYDSIKRCRDCGYQFTEDSDKCPRCGSENIDDKLETLEALRELALEVDEVLIATDPDTEGEKIAWDVYLALRPY-----N  147 (170)
T ss_pred             eeeEeeccCCcccccccccccCCcCCCcCCcchHHHHHHHHHHHhhCCEEEEecCCCccHHHHHHHHHHHhccC-----C
Confidence                    110 1121     22211 11123457889999999999999999999999999999999999632     5


Q ss_pred             CcEEEEEecccCHHHHHHHHHhC
Q psy8714         141 KTVWRARFSAITDKDIKAAMWNL  163 (562)
Q Consensus       141 ~~v~Rl~~sslt~~~I~~A~~nl  163 (562)
                      ++++|+|||++|+++|++||+||
T Consensus       148 ~~v~R~~fs~it~~~I~~a~~n~  170 (170)
T cd03361         148 KNIKRAEFHEVTRRAILEALRNP  170 (170)
T ss_pred             CCeEEEEEecCCHHHHHHHHhCc
Confidence            78999999999999999999986

Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.

>cd03363 TOPRIM_TopoIA_TopoI TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to Escherichia coli DNA topoisomerase I

Probab=99.96  E-value=3.8e-29  Score=224.23  Aligned_cols=123  Identities=28%  Similarity=0.283  Sum_probs=100.0

Q ss_pred             eEEEEecccCcCCcchHHhhcccccCCCCceeeeeeeeEcCCCcEEEEEEecccccccccccCCCCCccCCCCCCCCCCc
Q psy8714           6 KKLVPASEIKLARPSLISLLTPLQRMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPT   85 (562)
Q Consensus         6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~~~~~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~~~~y~~W~~~~p~~~~~~~~   85 (562)
                      |+||||||     ||+|+.|++++|.                  .|+|+||.|||++|..|++|..|.. .|.. +..  
T Consensus         1 ~~LiIaEK-----p~~a~~ia~~Lg~------------------~~~v~~~~GHl~~l~~p~~~~~~~~-~~~~-~~~--   53 (123)
T cd03363           1 KKLVIVES-----PAKAKTIKKYLGK------------------EYEVLASVGHIRDLPKKGLGVDGED-DGFE-PKY--   53 (123)
T ss_pred             CEEEEEeC-----HHHHHHHHHHhCC------------------CcEEEeccCccccCCCcccCCChhc-cCcC-ceE--
Confidence            78999999     9999999988764                  2679999999999998888865431 2211 111  


Q ss_pred             ccccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHHHHHhC
Q psy8714          86 EKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNL  163 (562)
Q Consensus        86 ~~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~A~~nl  163 (562)
                       . ....+.++++.|+++++++|+||||||||||||+|+|+|+++++      ++++|+|+|||++|+++|++||+||
T Consensus        54 -~-~~~~~~~~~~~ik~l~~~~~eiiiAtD~drEGe~i~~~i~~~~~------~~~~v~Rl~~sslt~~~I~~A~~n~  123 (123)
T cd03363          54 -V-VIPGKKKVVKELKKLAKKADEIYLATDPDREGEAIAWHLAEVLK------LKKNVKRVVFNEITKEAIKEALKNP  123 (123)
T ss_pred             -E-ECccHHHHHHHHHHHHhcCCEEEEcCCCCcchHHHHHHHHHHcC------CCCCeEEEEEccCCHHHHHHHHhCc
Confidence             0 11223467788888889999999999999999999999999995      3589999999999999999999985

Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.

>PF01751 Toprim: Toprim domain; InterPro: IPR006171 This is a conserved region from DNA primase

Probab=99.81  E-value=6e-21  Score=165.30  Aligned_cols=98  Identities=24%  Similarity=0.383  Sum_probs=81.4

Q ss_pred             EEEEecccCcCCcchHHhhcccccCCCCceeeeeeeeEcCCCcEEEEEEecccccccccccCCCCCccCCCCCCCCCCcc
Q psy8714           7 KLVPASEIKLARPSLISLLTPLQRMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPTE   86 (562)
Q Consensus         7 ~l~~ae~~~~~~p~~a~~~~~~~g~~~~~~~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~~~~y~~W~~~~p~~~~~~~~~   86 (562)
                      +|||+|+     |+.|+.++++++               +.  .+.|+|+.||++++..|+.|..               
T Consensus         1 ~liIvE~-----ps~a~~i~~~l~---------------~~--~~~v~~~~Ghl~~~~~~~~~~~---------------   43 (100)
T PF01751_consen    1 ELIIVEK-----PSDAKAIAKALG---------------GE--EYIVIATSGHLLELAKPEDYDP---------------   43 (100)
T ss_dssp             EEEEESS-----HHHHHHHHHHSS---------------TT--TEEEEEESSSSEESTTSSHHHC---------------
T ss_pred             CEEEEeC-----HHHHHHHHHHcC---------------CC--CEEEEEeCCccccccccccccc---------------
Confidence            6999999     999999998777               22  2579999999999998887642               


Q ss_pred             cccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCc--EEEEEeccc
Q psy8714          87 KREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKT--VWRARFSAI  151 (562)
Q Consensus        87 ~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~--v~Rl~~ssl  151 (562)
                          ..+.+.++.|+++++++|+||+|||||||||+|+|+|+++++..      .|  ++|+||||+
T Consensus        44 ----~~~~~~i~~l~~~~~~~~~iiiatD~D~EGe~Ia~~i~~~~~~~------~~~~~~R~~~~~i  100 (100)
T PF01751_consen   44 ----KDKKKQIKNLKKLLKKADEIIIATDPDREGELIAWEIIELLGKN------NPKLIKRVWFSSI  100 (100)
T ss_dssp             ----HTTHHHHHHHHHHHHSCSEEEEEC-SSHHHHHHHHHHHHHHHHH------SHHHTTEEEEESS
T ss_pred             ----ccccccchhhHHHhhhccEeeecCCCChHHHHHHHHHHHHHhHh------CCCcCCEEEEecC
Confidence                12346788888888899999999999999999999999999764      33  699999986

This corresponds to the Toprim (topoisomerase-primase) domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR/M DNA repair proteins []. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase 2.7.7.6 from EC is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division []. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases []. Type II DNA topoisomerases catalyse the relaxation of DNA supercoiling by causing transient double strand breaks.; PDB: 2ZJT_A 3IG0_A 3M4I_A 3NUH_B 1GKU_B 1GL9_C 3PWT_A 1CY4_A 1ECL_A 1CY7_A ....

>cd01025 TOPRIM_recR TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in Escherichia coli RecR

Probab=97.95  E-value=4.1e-05  Score=67.31  Aligned_cols=38  Identities=16%  Similarity=0.125  Sum_probs=32.8

Q ss_pred             cCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEe
Q psy8714         106 DCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARF  148 (562)
Q Consensus       106 ~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~  148 (562)
                      +.++||+|||||+|||.+++.|.+.++..     ..+|.|+-+
T Consensus        56 ~i~EVIlA~~pt~EGe~Ta~yi~~~l~~~-----~~kvsRlA~   93 (112)
T cd01025          56 QVKEVILATNPTVEGEATALYIAKLLKDF-----GVKVTRLAQ   93 (112)
T ss_pred             CCcEEEEecCCCchHHHHHHHHHHHHhHc-----CCCeEEEEE
Confidence            56899999999999999999999999753     567888854

RecR participates in the RecFOR pathway of homologous recombinational repair in prokaryotes. This pathway provides a single-stranded DNA molecule coated with RecA to allow invasion of a homologous molecule. The RecFOR system directs the loading of RecA onto gapped DNA coated with SSB protein. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). In RecR sequences this glutamate in the first turn of the TOPRIM domain is semiconserved, the DXD motif is not conserved.

>smart00493 TOPRIM topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins

Probab=97.89  E-value=2.1e-05  Score=63.97  Aligned_cols=72  Identities=24%  Similarity=0.289  Sum_probs=50.5

Q ss_pred             eEEEEecccCcCCcchHHhhcccccCCCCceeeeeeeeEcCCCcEEEEEEecccccccccccCCCCCccCCCCCCCCCCc
Q psy8714           6 KKLVPASEIKLARPSLISLLTPLQRMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPT   85 (562)
Q Consensus         6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~~~~~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~~~~y~~W~~~~p~~~~~~~~   85 (562)
                      ++|||+|.     |.-|..+....+                .  .+.+.++.||+...                      
T Consensus         1 ~~l~ivEg-----~~da~~~~~~~~----------------~--~~~~~~~~G~~~~~----------------------   35 (76)
T smart00493        1 KVLIIVEG-----PADAIALEKAGG----------------F--GGNVVALGGHLLKK----------------------   35 (76)
T ss_pred             CEEEEEcC-----HHHHHHHHHhcC----------------C--CEEEEEEeeeecHH----------------------
Confidence            57999999     777777764222                0  13467888997210                      


Q ss_pred             ccccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHh
Q psy8714          86 EKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVR  132 (562)
Q Consensus        86 ~~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~  132 (562)
                               +.++.|++...+ ++||+|+|+|+||+.+++++.+++.
T Consensus        36 ---------~~~~~l~~~~~~-~~Iii~~D~D~~G~~~~~~i~~~l~   72 (76)
T smart00493       36 ---------EIIKLLKRLAKK-KEVILATDPDREGEAIAWKLAELLK   72 (76)
T ss_pred             ---------HHHHHHHHHhcC-CEEEEEcCCChhHHHHHHHHHHHhh
Confidence                     133344443334 7899999999999999999999885

>PRK00076 recR recombination protein RecR; Reviewed

Probab=96.57  E-value=0.019  Score=55.57  Aligned_cols=55  Identities=13%  Similarity=0.099  Sum_probs=44.0

Q ss_pred             ccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEe--------cccCHHHHHHHHHhCC
Q psy8714         105 KDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARF--------SAITDKDIKAAMWNLV  164 (562)
Q Consensus       105 ~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~--------sslt~~~I~~A~~nl~  164 (562)
                      .++++||+||+|+.|||..++.|.+.++..     ...|.|+=.        .=++.-.+.+||++-+
T Consensus       132 ~~v~EVIlA~~pt~EGe~Ta~yi~~~lk~~-----~ikvtRiA~GiP~G~~ley~D~~TL~~Al~~R~  194 (196)
T PRK00076        132 GEVKEVILATNPTVEGEATAHYIARLLKPL-----GVKVTRLAHGVPVGGELEYVDEGTLSRALEGRR  194 (196)
T ss_pred             CCCCEEEEeCCCCchHHHHHHHHHHHHHHc-----CCCeeeeeeCCCCCcceeeCCHHHHHHHHHhCc
Confidence            468999999999999999999999999753     467888753        3456777788887654

>cd01027 TOPRIM_RNase_M5_like TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in Ribonuclease M5: (RNase M5) and other small primase-like proteins from bacteria and archaea

Probab=96.09  E-value=0.0079  Score=49.97  Aligned_cols=36  Identities=22%  Similarity=0.230  Sum_probs=29.2

Q ss_pred             CCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEE
Q psy8714         107 CEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRAR  147 (562)
Q Consensus       107 ~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~  147 (562)
                      .+.||++||+|+.|+.|.+.+.+.++.     +...++|+.
T Consensus        45 ~~~VIiltD~D~aG~~i~~~~~~~l~~-----~~~~~~~~~   80 (81)
T cd01027          45 YRGVIILTDPDRKGEKIRKKLSEYLSG-----PVPEIKRAF   80 (81)
T ss_pred             CCEEEEEECCCHHHHHHHHHHHHHhcc-----cCCCeeecc
Confidence            689999999999999999999999853     234466653

RNase M5 catalyzes the maturation of 5S rRNA in low G+C Gram-positive bacteria. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.

>cd00188 TOPRIM Topoisomerase-primase domain

Probab=95.79  E-value=0.041  Score=43.92  Aligned_cols=36  Identities=28%  Similarity=0.446  Sum_probs=28.7

Q ss_pred             CCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEE
Q psy8714         107 CEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRAR  147 (562)
Q Consensus       107 ~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~  147 (562)
                      +..|++++|+|.+|+.+++.+.+.+...     ...+.|++
T Consensus        47 ~~~v~i~~D~D~~g~~~~~~~~~~~~~~-----~~~~~~~~   82 (83)
T cd00188          47 AKEVIIATDADREGEAIALRLLELLKSL-----GKKVRRLL   82 (83)
T ss_pred             CCEEEEEcCCChhHHHHHHHHHHHHHhc-----CCceEEee
Confidence            6799999999999999999999887531     35566654

This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from bacterial and archaea, and bacterial DNA repair proteins of the RecR/M family. This domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases and in strand joining in topoisomerases and, as a general acid in strand cleavage by topisomerases and nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.

>smart00437 TOP1Ac Bacterial DNA topoisomerase I DNA-binding domain

Probab=92.30  E-value=0.38  Score=48.90  Aligned_cols=109  Identities=17%  Similarity=0.306  Sum_probs=68.6

Q ss_pred             hhhhhhhhhhhccc-CcceEEEEEEEeeCCeEEEEEee----cc--cccCH--HHHHHHHHHhhhcCceEEEEEEcceee
Q psy8714         219 GFCVERHDKIRTFK-PEPYWLLDLTLNLNGVAVSVTWS----RG--HIFDK--STCNVFFKAVEKEKHVTVVDVQSSTKS  289 (562)
Q Consensus       219 ~lIv~Re~eI~~F~-p~~y~~i~~~~~~~~~~~~~~~~----~~--~~~~~--~~a~~~~~~~~~~~~~~V~~v~~~~~~  289 (562)
                      .||+.|..+  +|= +..|-...+.+..++..|.+...    .|  .++..  .+.+..+-.+.....+.|.+++..++.
T Consensus       126 ~lI~rr~la--~~~~~~~~~~t~v~~~~~~~~F~a~g~~i~~~Gw~~v~~~~~~~~~~~lp~~~~g~~~~~~~~~~~e~~  203 (259)
T smart00437      126 ELIWRRFLA--SQMPDAKYEETKVIIKIGGEKFKAKGKTLLFDGWLKVYPEEKKEEEIELPTLKKGDELKVEEVEVEEKK  203 (259)
T ss_pred             HHHHHHHHH--HhChhheEEEEEEEEEECCeEEEEEEEEEeECCHHHhhcccccCccccCCCcCCCCEeeeeeeEEEecc
Confidence            455555543  333 34455566667667777766532    11  12111  111111222333346788888889999


Q ss_pred             ccCCCCCCHHHHHHHHHhhCCCCHHHH-HHHHHHhHhcCcee
Q psy8714         290 KTKPQALNTVELMRVASSGLGMGPHHA-MQIAERLYTQGYVS  330 (562)
Q Consensus       290 ~~pP~pf~l~~Lq~~a~~~~g~s~~~t-l~iaQ~LYE~glIS  330 (562)
                      +.||.+|+-++|...+-+ .|+.-.-| ..+.+.|.++|||.
T Consensus       204 TkPP~~~Te~tLl~~Me~-~GIGTpATra~iIe~L~~r~Yi~  244 (259)
T smart00437      204 TKPPARYTEASLIKLMEK-RGIGRPSTYAEIIETLLDRGYVT  244 (259)
T ss_pred             cCCCCCCCHHHHHHHHHH-CCCCchhhHHHHHHHHHhCCcEE
Confidence            999999999999999864 58764444 46699999999996

Bacterial DNA topoisomerase I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase alpha subunit

>PF13662 Toprim_4: Toprim domain; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A

Probab=92.13  E-value=0.095  Score=43.17  Aligned_cols=35  Identities=20%  Similarity=0.234  Sum_probs=23.4

Q ss_pred             CCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEE
Q psy8714         107 CEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRA  146 (562)
Q Consensus       107 ~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl  146 (562)
                      ..+||+|+|+|.+|+..+.++.+.+...     ..+|+|+
T Consensus        46 ~~~Vii~~D~D~~G~~~a~~i~~~l~~~-----gi~v~~v   80 (81)
T PF13662_consen   46 VKEVIIAFDNDKAGEKAAQKIAKKLLPL-----GIRVTRV   80 (81)
T ss_dssp             -SEEEEEEESSHHHHHHHHHHHHHHG--------------
T ss_pred             CceEEEEeCcCHHHHHHHHHHHHHHHhh-----ccccccC
Confidence            5789999999999999999999977532     3556664

>PRK13844 recombination protein RecR; Provisional

Probab=91.50  E-value=0.62  Score=45.26  Aligned_cols=53  Identities=13%  Similarity=0.167  Sum_probs=42.1

Q ss_pred             cCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEe--------cccCHHHHHHHHHhCC
Q psy8714         106 DCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARF--------SAITDKDIKAAMWNLV  164 (562)
Q Consensus       106 ~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~--------sslt~~~I~~A~~nl~  164 (562)
                      ++++||+||.|+-|||.-+..|.+.++     + ...|.|+=.        .=++...+.+||++-+
T Consensus       138 ~v~EVIlAt~~t~EGe~Ta~yi~~~lk-----~-~vkvtRlA~GiP~G~~ley~D~~TL~~Al~~R~  198 (200)
T PRK13844        138 KIDEVILAISPTVEGETTAHFISQMIA-----K-DIKISRIGFGVPFGGELEYLDQQTLLHAFNART  198 (200)
T ss_pred             CCcEEEEeCCCCccHHHHHHHHHHHhc-----C-CCcEEeeeecCcCCcceeecCHHHHHHHHHhCc
Confidence            689999999999999999999999885     2 466778742        3456777888887754

>TIGR01057 topA_arch DNA topoisomerase I, archaeal

Probab=91.03  E-value=0.51  Score=53.95  Aligned_cols=131  Identities=9%  Similarity=0.120  Sum_probs=80.6

Q ss_pred             HHHHHHHHHHh--hcccCceEEEEEEEEEECCeEEEEEEEEEeecceeeeecccccccCCCCCCCCCCeeeeeeeEEeee
Q psy8714         403 LYDYIVRHFIG--TLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKMVER  480 (562)
Q Consensus       403 vY~lI~rr~la--~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~v~~~~~~~~~~Lp~l~~G~~~~~~~~~i~e~  480 (562)
                      +-.+|+.|..+  .|- |..|=...+.+..++..|.+....    +  .+...+.. +..+-.++..+...+.++.-+++
T Consensus       196 tL~lvv~Re~eI~~F~-p~~y~~i~~~~~~~~~~~~~~~~~----~--~~~~~~~a-~~~~~~~~~~~~~~V~~v~~~~~  267 (618)
T TIGR01057       196 TLAFLVEREREINLFV-PKPYWVIKATLEKGGGVFDARPEK----W--KIWSEEEA-KSIKEELKKSPWAAVEEVRSERS  267 (618)
T ss_pred             HHHHHHHhHHHHHcCc-CCccEEEEEEEecCCceEEEEEcc----C--CcCCHHHH-HHHHHHHhCCCCeEEEEEEeeee
Confidence            33567777665  444 444445556666666667665310    0  11111100 11112233333577888999999


Q ss_pred             ecCCCCCCCHHHHHHHHH-hcCCCCcCchhHHHHHhhcCCeEEE-cCCCeeecchhH-HHHHHhh
Q psy8714         481 KTTPPDYLTESELISLME-KHGIGTDASIPVHINNICQRNYVTV-TSGRRLVPTSLG-IVLVHGY  542 (562)
Q Consensus       481 ~TkPP~~~Te~~Li~~Me-~~GIGTpATra~iI~~L~~r~Yi~~-~~~k~l~~T~~G-~~li~~l  542 (562)
                      ++.||.+|+-++|.+.|- +.|++..-|. .|.++|.+.|||.- ......+|.+.. ..+++.+
T Consensus       268 ~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl-~iaQ~LYe~g~ISYPRTds~~l~~~~~~~~~l~~l  331 (618)
T TIGR01057       268 ILKPPPPFDLGTLQREAYRIFGFSPKKTQ-SIAQELYEEALISYPRTSSQKLPPSINYRAILDNL  331 (618)
T ss_pred             eccCCCCccHHHHHHHHHHhcCCCHHHHH-HHHHHHHhcCceeecCcccCccCHHHhHHHHHHHH
Confidence            999999999999999775 5699998888 79999999999973 122345555532 3344443

This model describes topoisomerase I from archaea. These enzymes are involved in the control of DNA topology. DNA topoisomerase I belongs to the type I topoisomerases, which are ATP-independent.

>PF01131 Topoisom_bac: DNA topoisomerase; InterPro: IPR013497 DNA topoisomerases regulate the number of topological links between two DNA strands (i

Probab=91.02  E-value=0.55  Score=50.83  Aligned_cols=114  Identities=15%  Similarity=0.278  Sum_probs=69.5

Q ss_pred             chhhhhhhhhhhhcccCcceEEEEEEEeeCCeEEEEEeec----c--cccCHHHHHH---HHHHhhhcCceEEEEEEcce
Q psy8714         217 TLGFCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSR----G--HIFDKSTCNV---FFKAVEKEKHVTVVDVQSST  287 (562)
Q Consensus       217 tL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~~----~--~~~~~~~a~~---~~~~~~~~~~~~V~~v~~~~  287 (562)
                      +-.+|+.|..+. -+.|..|-...+.+..++..|.+....    |  .+......+.   .+..+.....+.+.++..++
T Consensus       228 vY~LI~rr~la~-~~~~~~~~~t~v~~~~~~~~F~~~g~~~~~~Gw~~~~~~~~~~~~~~~lp~l~~g~~~~~~~~~~~e  306 (403)
T PF01131_consen  228 VYDLIARRFLAA-FMPDAKYEKTTVTFEVGGEEFKASGKVIIDPGWKKVYPYEEEEDEEEDLPSLKEGDEIPIEDVEIKE  306 (403)
T ss_dssp             HHHHHHHHHHHH-TS--EEEEEEEEEEEETTEEEEEEEEEEEEHGGGGCS-HCHCCTTSBB-----TTEEEEEEEEEEEE
T ss_pred             HHHHHHHHHHHH-HHHHHheeeEEEEEEecCcEEEEEEeEEEECceeEEEEcccccccccccccccCCcEEeecccchhh
Confidence            345666665554 224455666778888888888876531    1  1222111111   23334444457788889999


Q ss_pred             eeccCCCCCCHHHHHHHHHhhCCCCHHHH-HHHHHHhHhcCceeec
Q psy8714         288 KSKTKPQALNTVELMRVASSGLGMGPHHA-MQIAERLYTQGYVSYP  332 (562)
Q Consensus       288 ~~~~pP~pf~l~~Lq~~a~~~~g~s~~~t-l~iaQ~LYE~glISYP  332 (562)
                      +.+.||.+|+-++|...+- ..|+.-.-| ..|.+.|.++|||.--
T Consensus       307 ~~TkPP~~~Te~~Ll~~Me-~~GIGTpATra~iI~~L~~r~Yi~~~  351 (403)
T PF01131_consen  307 KKTKPPKRYTEASLLKAME-KAGIGTPATRASIIEKLIKRGYIERS  351 (403)
T ss_dssp             EEEESS--EBHHHHHHHHH-HTTSS-TTTHHHHHHHHHHTTSEEE-
T ss_pred             hccCCCCCCCHHHHHhhhh-hcCCCccccHHHHHHHhhccceeecc
Confidence            9999999999999999884 568874444 5679999999999864

e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. Type IA topoisomerases are comprised of four domains that together form a toroidal structure with a central hole large enough to accommodate single- and double-stranded DNA: an N-terminal alpha/beta Toprim domain, domain 2 and the C-terminal domain 4 are winged-helix domains, and domain 3 is a beta-barrel. Domains 1 (Toprim) and 3 form the active site of the enzyme, while the winged helix domains 2 and 4 form a single-strand DNA-binding groove [, ]. This entry represents the central portion of the enzyme, which covers domains 2 and 3 in topoisomerase type IA enzymes. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome; PDB: 1CYY_A 3PWT_A 1CY4_A 1CY9_A 1ECL_A 1CY7_A 1CY8_A 1CY6_A 1MW8_X 1CY0_A ....

>TIGR00615 recR recombination protein RecR

Probab=90.51  E-value=0.46  Score=45.99  Aligned_cols=52  Identities=13%  Similarity=0.077  Sum_probs=40.6

Q ss_pred             cCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEe--------cccCHHHHHHHHHh
Q psy8714         106 DCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARF--------SAITDKDIKAAMWN  162 (562)
Q Consensus       106 ~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~--------sslt~~~I~~A~~n  162 (562)
                      ++++||+||+|+-|||.-+..|.+.++..     ..+|.|+=.        .=++.-.+.+||++
T Consensus       134 ~v~EVIlAt~~tvEGe~Ta~yi~~~lk~~-----~ikvtRlA~GiP~G~~ley~D~~TL~~Al~~  193 (195)
T TIGR00615       134 SVKEVILATNPTVEGEATALYIARLLQPF-----GVKVTRIASGLPVGGDLEYADEVTLARALEG  193 (195)
T ss_pred             CCcEEEEeCCCCchHHHHHHHHHHHhhhc-----CCcEEeeeecCCCCcceeecCHHHHHHHHHc
Confidence            58999999999999999999999998742     467888742        33566667777765

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>COG1658 Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]

Probab=89.60  E-value=0.45  Score=42.91  Aligned_cols=68  Identities=10%  Similarity=0.136  Sum_probs=44.5

Q ss_pred             hHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhccc----CCCCc---EEE-EEecccCHHHHHHHHHhCC
Q psy8714          96 LPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQINI----NSPKT---VWR-ARFSAITDKDIKAAMWNLV  164 (562)
Q Consensus        96 ~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~----~~~~~---v~R-l~~sslt~~~I~~A~~nl~  164 (562)
                      .+..|+++ .+-..||+-||||+.||-|...+.+++.....-    ....+   ..| +-+-++....++.|+.+..
T Consensus        45 ~ie~i~~~-~~~k~VIILTD~D~~Ge~Irk~l~~~l~~~~~~~id~~~~~~~~~~~~i~gVE~~~~~~~~~~l~~~~  120 (127)
T COG1658          45 TIELIKKA-QKYKGVIILTDPDRKGERIRKKLKEYLPGAKGAFIDREIRNKLKINGKIIGVEEASSEALRKALKEVP  120 (127)
T ss_pred             HHHHHHHh-hccCCEEEEeCCCcchHHHHHHHHHHhcccccccccHHHhhhcccccccccceecChHHHHHHHHhCC
Confidence            44455543 244579999999999999999999998652110    00111   222 2345788888888888765

>TIGR00334 5S_RNA_mat_M5 ribonuclease M5

Probab=88.89  E-value=1.1  Score=42.45  Aligned_cols=69  Identities=14%  Similarity=0.077  Sum_probs=44.5

Q ss_pred             hHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhc----ccCCCCc-EEEEEecccCHHHHHHHHHhCCC
Q psy8714          96 LPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQI----NINSPKT-VWRARFSAITDKDIKAAMWNLVK  165 (562)
Q Consensus        96 ~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~----~~~~~~~-v~Rl~~sslt~~~I~~A~~nl~~  165 (562)
                      .++.|+.+. +-.-||+-||||.-||.|=..|.+++....    .+....+ =.-+=+-..++++|++|+.+...
T Consensus        37 ~i~~i~~~~-~~rgVIIfTDpD~~GekIRk~i~~~vp~~khafi~~~~a~~~~~~iGVE~As~e~I~~AL~~~~~  110 (174)
T TIGR00334        37 TINLIKKAQ-KKQGVIILTDPDFPGEKIRKKIEQHLPGYENCFIPKHLAKPNKKKIGVEEASVEAIIAALENVHE  110 (174)
T ss_pred             HHHHHHHHh-hcCCEEEEeCCCCchHHHHHHHHHHCCCCeEEeeeHHhcCcCCCCcccCCCCHHHHHHHHHHhcc
Confidence            455565544 334699999999999999888877763210    0000000 01134556789999999999875

This family of orthologous proteins shows a weak but significant similarity to the central region of the DnaG-type DNA primase. The region of similarity is termed the Toprim (topoisomerase-primase) domain and is also shared by RecR, OLD family nucleases, and type IA and II topoisomerases.

>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]

Probab=88.76  E-value=1.1  Score=43.68  Aligned_cols=56  Identities=16%  Similarity=0.293  Sum_probs=42.2

Q ss_pred             hhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEec------ccCHHHHHHHHHh
Q psy8714         102 NEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFS------AITDKDIKAAMWN  162 (562)
Q Consensus       102 ~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~s------slt~~~I~~A~~n  162 (562)
                      ..+..||.|+||||+||-|--+|....+-++..     -+.|.||.+.      -++.+-|++-+.|
T Consensus        53 raaeGADlvlIATDaD~~GReLA~kf~eeLrg~-----VGhiERmK~PiGHDvEhiD~elvrkEl~n  114 (290)
T COG4026          53 RAAEGADLVLIATDADRVGRELAEKFFEELRGM-----VGHIERMKIPIGHDVEHIDVELVRKELKN  114 (290)
T ss_pred             HhhccCCEEEEeecCcchhHHHHHHHHHHHHHh-----hhhhheeccCCCCCccccCHHHHHHHHHH
Confidence            446799999999999999999999888888654     3668888763      3455555555554

>PRK04031 DNA primase; Provisional

Probab=88.40  E-value=0.6  Score=49.85  Aligned_cols=70  Identities=21%  Similarity=0.250  Sum_probs=48.9

Q ss_pred             HHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHHHHHhCCCChHhH
Q psy8714          97 PAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNLVKPNIFE  170 (562)
Q Consensus        97 i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~A~~nl~~~~~~l  170 (562)
                      -..+.++++ .+.|++++|+|+-|+.|.+++++.++..+-  .+.| .-.-.-++++++|.+|+.+..|..+.+
T Consensus       201 ~~~i~~l~k-~~~Vil~~DgD~aGe~I~k~l~~v~~~d~V--araP-~G~dVE~ls~eeI~kAL~~~~p~~~~l  270 (408)
T PRK04031        201 PETIIELSK-KKTVTAFLDGDRGGELILKELLQVADIDYV--ARAP-PGKEVEELTKKEIAKALRNKVPVEQYL  270 (408)
T ss_pred             HHHHHHHhc-CCCEEEEECCCHHHHHHHHHHHhhcceeEE--ecCC-CCCChhhCCHHHHHHHHHhcCCHHHHH
Confidence            345556555 789999999999999999999875321100  0111 112356889999999999988877664

>PRK07220 DNA topoisomerase I; Validated

Probab=88.25  E-value=1.4  Score=51.53  Aligned_cols=75  Identities=17%  Similarity=0.285  Sum_probs=54.8

Q ss_pred             CCeeeeeeeEEeeeecCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEE-cCCCeeecchh-HHHHHHhh
Q psy8714         467 GDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTV-TSGRRLVPTSL-GIVLVHGY  542 (562)
Q Consensus       467 G~~~~~~~~~i~e~~TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~-~~~k~l~~T~~-G~~li~~l  542 (562)
                      +..+.|.++..++++..||.+|+-++|..++-+.|+. |..-..|.+.|++.|||.- ......+|.+. ...+++.|
T Consensus       257 ~~~~~V~~v~~~~~~~~pP~pf~ts~Lq~~a~~~g~s-~~~tm~iaQ~LYe~g~ITYPRTDs~~l~~~~~~~~~i~~l  333 (740)
T PRK07220        257 GKTAEVTEVEKGTKTDKPPTPFNTTEFISAANSIGFS-AANAMRIAESLYTNGYISYPRTDNTVYPESLDLREQIEIF  333 (740)
T ss_pred             CCCeEEEEEeeeeEecCCCCCcCHHHHHHHHHHcCCC-HHHHHHHHHHHHhCCceeecccCCeecCchhhHHHHHHHH
Confidence            3457788899999999999999999999999877773 4444579999999999973 12345556543 33344433

>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]

Probab=86.02  E-value=1.5  Score=42.30  Aligned_cols=51  Identities=14%  Similarity=0.104  Sum_probs=38.0

Q ss_pred             CeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEe--------cccCHHHHHHHHHhC
Q psy8714         108 EFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARF--------SAITDKDIKAAMWNL  163 (562)
Q Consensus       108 d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~--------sslt~~~I~~A~~nl  163 (562)
                      ++||+||+|--|||.-+..|.+.+++.     ..+|.|+=.        -=+++-.+.+||.+-
T Consensus       137 ~EvIlAtnpTvEGeaTA~YI~~~l~~~-----~ikvtRlA~GiPvGg~lEyvD~~TL~~Al~~R  195 (198)
T COG0353         137 KEVILATNPTVEGEATALYIARLLKPL-----GLKVTRLAQGVPVGGELEYVDEGTLSRALEGR  195 (198)
T ss_pred             ceEEEecCCCccchHHHHHHHHHHhhc-----CCeEEEEeecCccCCceecccHHHHHHHHhcC
Confidence            399999999999999999999999764     567888742        223455555555543

>COG0550 TopA Topoisomerase IA [DNA replication, recombination, and repair]

Probab=85.96  E-value=2  Score=48.49  Aligned_cols=127  Identities=17%  Similarity=0.182  Sum_probs=77.6

Q ss_pred             HHHHHHH--hhcccCceEEEEEEEEEECCeEEEEEEEEEeecceeeeecccccccCCCCCCCCCCeeeeeeeEEeeeecC
Q psy8714         406 YIVRHFI--GTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKMVERKTT  483 (562)
Q Consensus       406 lI~rr~l--a~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~v~~~~~~~~~~Lp~l~~G~~~~~~~~~i~e~~Tk  483 (562)
                      ||+.|--  ..|- |..|-...+.+..++..|.+.-.......+..+...+.. ...+-.++ |+.+.|.+++-+.++..
T Consensus       179 lVveRE~EI~~F~-p~~yw~i~a~~~~~~~~f~a~~~~~~~~~~~~~~~~~~a-~~~~~~l~-~~~~~V~~ve~k~~~~~  255 (570)
T COG0550         179 LVVEREREIEAFV-PEEYWEIKAIFEKGGGEFSARLTEIEGKKEGRLKDKDEA-EEIVNKLK-GKPAKVVSVEKKPKKRS  255 (570)
T ss_pred             hhHhhHHHHHhCC-CCcceEEEEEEecCCccEEEEEeccccccccccccHHHH-HHHHHHcc-CCceEEEEEeeeeeccC
Confidence            3444433  3444 456667777777665557665443221111111110000 11122333 88888999999999999


Q ss_pred             CCCCCCHHHHHHHHHh-cCCCCcCchhHHHHHhhcC-CeEEE--cCCCeeecchhHH
Q psy8714         484 PPDYLTESELISLMEK-HGIGTDASIPVHINNICQR-NYVTV--TSGRRLVPTSLGI  536 (562)
Q Consensus       484 PP~~~Te~~Li~~Me~-~GIGTpATra~iI~~L~~r-~Yi~~--~~~k~l~~T~~G~  536 (562)
                      ||++||-++|....-+ .|++..-|. .|-++|++. |||.-  .....|-++-...
T Consensus       256 pp~Pf~tstLQq~As~~lgfs~kktm-~iAQ~LYE~~glITYpRTDs~~ls~~~~~~  311 (570)
T COG0550         256 PPPPFTTSTLQQEASRKLGFSAKKTM-DIAQKLYEGHGLITYPRTDSTRLSEEALAE  311 (570)
T ss_pred             CCCCCcHHHHHHHHHHhCCCCHHHHH-HHHHHHhcCCCcEEecCCCCCcCCHHHHHH
Confidence            9999999999988755 478877776 688999997 99973  3333444444443

>cd00186 TOP1Ac DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases

Probab=85.84  E-value=1.7  Score=46.75  Aligned_cols=110  Identities=17%  Similarity=0.278  Sum_probs=68.5

Q ss_pred             hhhhhhhhhhhcccCcceEEEEEEEeeCCeEEEEEee----cc--cccC--HHHHHHHHHHhhhcCceEEEEEEcceeec
Q psy8714         219 GFCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWS----RG--HIFD--KSTCNVFFKAVEKEKHVTVVDVQSSTKSK  290 (562)
Q Consensus       219 ~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~----~~--~~~~--~~~a~~~~~~~~~~~~~~V~~v~~~~~~~  290 (562)
                      .||+.|....- ..+.-|=...+.+..++..|.+...    .|  .+..  +...+..+-.+.....+.+.+++..++.+
T Consensus       199 ~LI~rrfla~~-~~~~~~~~t~v~~~~~~~~F~a~g~~i~~~Gw~~v~~~~~~~~~~~~p~l~~g~~~~~~~~~~~~~~T  277 (381)
T cd00186         199 ELIWRRFLASQ-MADAKYEETTVTLEIGGEKFKASGKVLLEDGWLEVYPEEKDDEEEEPPPLKEGDELKLEEVELEEKET  277 (381)
T ss_pred             HHHHHHHHHHh-CchhhEEEEEEEEEECCeEEEEEEEEEeeCCHHHHhCcccccccccCCCCCCCCEEeeeeeeeeeccc
Confidence            46666665442 2344455566777666667766431    11  1111  11001111123333456778888889999


Q ss_pred             cCCCCCCHHHHHHHHHhhCCCCHHHHH-HHHHHhHhcCcee
Q psy8714         291 TKPQALNTVELMRVASSGLGMGPHHAM-QIAERLYTQGYVS  330 (562)
Q Consensus       291 ~pP~pf~l~~Lq~~a~~~~g~s~~~tl-~iaQ~LYE~glIS  330 (562)
                      .||.+|+-++|..++- ..|+.-.-|. .|.+.|.++|||.
T Consensus       278 ~PP~~~Te~~Li~~Me-~~GIGTpATra~iI~~L~~r~Yi~  317 (381)
T cd00186         278 QPPPRYTEASLIKLME-KRGIGRPSTYASIIETLLDRGYVE  317 (381)
T ss_pred             CCCCCCCHHHHHHHHH-hCCCCccccHHHHHHHHHhCCcEE
Confidence            9999999999999885 4588755554 5699999999997

Topoisomerases clevage single or double stranded DNA and then rejoin the broken phosphodiester backbone. Proposed catalytic mechanism of single stranded DNA cleavage is by phosphoryl transfer through a tyrosine nucleophile using acid/base catalysis. Tyr is activated by a nearby group (not yet identified) acting as a general base for nucleophilic attack on the 5' phosphate of the scissile bond. Arg and Lys stabilize the pentavalent transition state. Glu then acts as a proton donor for the leaving 3'-oxygen, upon cleavage of the scissile strand.

>TIGR01051 topA_bact DNA topoisomerase I, bacterial

Probab=85.50  E-value=2.6  Score=48.24  Aligned_cols=118  Identities=16%  Similarity=0.287  Sum_probs=70.6

Q ss_pred             hhhhhhhhhhccc-CcceEEEEEEEee--CCeEEEEEee----cc--ccc--C----HHHHHHHHHHhhhcCceEEEEEE
Q psy8714         220 FCVERHDKIRTFK-PEPYWLLDLTLNL--NGVAVSVTWS----RG--HIF--D----KSTCNVFFKAVEKEKHVTVVDVQ  284 (562)
Q Consensus       220 lIv~Re~eI~~F~-p~~y~~i~~~~~~--~~~~~~~~~~----~~--~~~--~----~~~a~~~~~~~~~~~~~~V~~v~  284 (562)
                      ||+.|...  +|- |.-|-+..+.+..  ++..|.+...    .|  .++  +    ++..+..+-.+.....+.+.+++
T Consensus       372 lI~rr~la--~~~~~~~~~~t~v~~~~~~~~~~F~a~g~~i~~~Gw~~v~~~~~~~~~~~~~~~Lp~l~~g~~~~~~~~~  449 (610)
T TIGR01051       372 LIWKRFVA--SQMADARYDSTSVRLTNEDGEYVFKATGRKLIFDGYYKVYVEGSDDPLEEKDRILPPLKEGDAVKLVEVK  449 (610)
T ss_pred             HHHHHHHH--HhCccceEEEEEEEEEEcCCCeEEEEEEEEEEeCCHHHhcccccccccccccccCCCCCCCCEeEeeeee
Confidence            45555543  343 4455556666665  5556765431    11  011  0    01111122233333456777888


Q ss_pred             cceeeccCCCCCCHHHHHHHHHhhCCCCHHHHH-HHHHHhHhcCceeecCCCCCCCCCc
Q psy8714         285 SSTKSKTKPQALNTVELMRVASSGLGMGPHHAM-QIAERLYTQGYVSYPRTETTQYPEN  342 (562)
Q Consensus       285 ~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl-~iaQ~LYE~glISYPRTds~~l~~~  342 (562)
                      ..++.+.||.+|+-++|..+|-+ .|+...-|. .+.+.|.++|||.  +-...-+|.+
T Consensus       450 ~~~~~T~PP~~yTe~tLl~~Me~-~GIGTpATra~iIe~L~~r~Yi~--~~~~~l~pT~  505 (610)
T TIGR01051       450 PNQHFTQPPARYTEASLVKELEE-LGIGRPSTYASIISTIQDRGYVK--KENKRLYPTE  505 (610)
T ss_pred             eccccccCCCCCCHHHHHHHHhc-CCCCccccHHHHHHHHhhCCeEE--eeCCEEeECH
Confidence            88899999999999999999854 587655554 5699999999998  3333344443

This model describes DNA topoisomerase I among the members of bacteria. DNA topoisomerase I transiently cleaves one DNA strand and thus relaxes negatively supercoiled DNA during replication, transcription and recombination events.

>PRK05776 DNA topoisomerase I; Provisional

Probab=85.46  E-value=2.2  Score=49.28  Aligned_cols=109  Identities=14%  Similarity=0.154  Sum_probs=69.8

Q ss_pred             HHHHHHHHh--hcccCceEEEEEEEEEECCeEEEEEEEEEeecceeeeecccccccCCCCCCCCCCeeeeeeeEEeeeec
Q psy8714         405 DYIVRHFIG--TLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKMVERKT  482 (562)
Q Consensus       405 ~lI~rr~la--~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~v~~~~~~~~~~Lp~l~~G~~~~~~~~~i~e~~T  482 (562)
                      .||+.|..+  .|-| ..|=...+.+..++..|.+.-.     +++ +...+.. +..+-.++....+.|.++..++++.
T Consensus       201 ~lVveRe~eI~~Fvp-~~yw~i~~~~~~~~~~f~~~~~-----~~~-~~~~~~a-~~i~~~~~~~~~~~V~~v~~k~~~~  272 (670)
T PRK05776        201 KYVVEREIERNLFVP-LPYFSVSIIIEKNGYEFTLKYE-----NKK-FETKEEA-KEILEEIKKTGYLKVTKVEVKIEIL  272 (670)
T ss_pred             hHhHhhHHHHHcCCC-CcceEEEEEEecCCceEEEEEc-----CCc-cCCHHHH-HHHHHHhcCCCCEEEEEEEeeeEEc
Confidence            456666554  4443 3344455556556656766531     222 2111100 1111223322457788999999999


Q ss_pred             CCCCCCCHHHHHHHHH-hcCCCCcCchhHHHHHhhcCCeEE
Q psy8714         483 TPPDYLTESELISLME-KHGIGTDASIPVHINNICQRNYVT  522 (562)
Q Consensus       483 kPP~~~Te~~Li~~Me-~~GIGTpATra~iI~~L~~r~Yi~  522 (562)
                      .||++|+-++|...+- +.|++..-|.. |.+.|.+.|||.
T Consensus       273 ~pP~pf~ts~LQ~~As~~lg~sa~ktm~-iAQ~LYe~glIS  312 (670)
T PRK05776        273 EPPPPFNLGDLQVEAARIYGFSPYKTQS-IAEDLYLDGLIS  312 (670)
T ss_pred             CCCCCCCHHHHHHHHHhhcCCCHHHHHH-HHHHHHhcCcee
Confidence            9999999999999885 45888877774 999999999997

>PRK07219 DNA topoisomerase I; Validated

Probab=85.37  E-value=1.9  Score=51.06  Aligned_cols=119  Identities=20%  Similarity=0.363  Sum_probs=75.0

Q ss_pred             hhhhhhhhhhhcccCcceEEEEEEEeeCCeEEEEEee----cc--cccCHHHH-HHHHHHhhhcCceEEEEEEcceeecc
Q psy8714         219 GFCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWS----RG--HIFDKSTC-NVFFKAVEKEKHVTVVDVQSSTKSKT  291 (562)
Q Consensus       219 ~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~----~~--~~~~~~~a-~~~~~~~~~~~~~~V~~v~~~~~~~~  291 (562)
                      .||+.|..... ..|..|=+..+.+..++..|.+...    .|  .++..+.. +..+-.+.....+.+.+++.+++.+.
T Consensus       394 ~LI~rrfla~~-~~~a~~~~t~v~~~~~~~~F~a~g~~i~~~Gw~~vy~~~~~~~~~lP~l~~G~~~~~~~~~~~~~~T~  472 (822)
T PRK07219        394 ELIVRRFLATL-ADPAEWEYLKVELDVNGEIFKASGSRLVEEGWHEVYPYEKFDEKELPDLEEGEKLKVNKIEIEAKETQ  472 (822)
T ss_pred             HHHHHHHHHHh-CccceeeEEEEEEEeCCeEEEEEEEEEccCCcHhhcCccccccccCCCCCCCCEeeeeeeEecccccC
Confidence            46777766553 2555666667777777777876542    11  11110000 11122233334567878888899999


Q ss_pred             CCCCCCHHHHHHHHHhhCCCCHHHH-HHHHHHhHhcCceeecCCCCCCCCCc
Q psy8714         292 KPQALNTVELMRVASSGLGMGPHHA-MQIAERLYTQGYVSYPRTETTQYPEN  342 (562)
Q Consensus       292 pP~pf~l~~Lq~~a~~~~g~s~~~t-l~iaQ~LYE~glISYPRTds~~l~~~  342 (562)
                      ||.+|+-++|.+++-+ .|+.-.-| ..|.+.|+++|||   +-.....|.+
T Consensus       473 PP~rytea~Li~~Me~-~GIGT~ATra~iI~~L~~R~Yv---~~~~~l~pT~  520 (822)
T PRK07219        473 PPKRYTQSSLIKEMEK-RGLGTKATRHDIIEKLYKRGYV---IEGDPPRPTD  520 (822)
T ss_pred             CCCCCCHHHHHHHHHh-CCCCCCccHHHHHHHHHhcCcE---ecCCEeeecH
Confidence            9999999999999854 58764444 5679999999999   4444444443

>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A

Probab=84.38  E-value=0.87  Score=37.26  Aligned_cols=39  Identities=5%  Similarity=0.185  Sum_probs=31.3

Q ss_pred             CchhHHHHHhhcCCeEEEcCCCeeecchhHHHHHHhhhcc
Q psy8714         506 ASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKI  545 (562)
Q Consensus       506 ATra~iI~~L~~r~Yi~~~~~k~l~~T~~G~~li~~l~~~  545 (562)
                      .+-..+|+.|.++|+|.. .++.+..|++|..+++.++.+
T Consensus        34 ~~~~~yL~~L~~~gLI~~-~~~~Y~lTekG~~~l~~l~~~   72 (77)
T PF14947_consen   34 STLKKYLKELEEKGLIKK-KDGKYRLTEKGKEFLEELEEL   72 (77)
T ss_dssp             HHHHHHHHHHHHTTSEEE-ETTEEEE-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCcCeeC-CCCEEEECccHHHHHHHHHHH
Confidence            344569999999999986 567999999999999887543

>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element

Probab=84.27  E-value=1.7  Score=36.59  Aligned_cols=44  Identities=14%  Similarity=0.198  Sum_probs=36.8

Q ss_pred             HhcCCCCcCchhHHHHHhhcCCeEEEcCCCeeecchhHHHHHHhh
Q psy8714         498 EKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGY  542 (562)
Q Consensus       498 e~~GIGTpATra~iI~~L~~r~Yi~~~~~k~l~~T~~G~~li~~l  542 (562)
                      +..|| +++|-..++..|.+.|||.+..++.+.+|+.|..+++.+
T Consensus         7 ~~l~i-s~stvs~~l~~L~~~glI~r~~~~~~~lT~~g~~~~~~~   50 (96)
T smart00529        7 ERLNV-SPPTVTQMLKKLEKDGLVEYEPYRGITLTEKGRRLARRL   50 (96)
T ss_pred             HHhCC-ChHHHHHHHHHHHHCCCEEEcCCCceEechhHHHHHHHH
Confidence            34577 788888999999999999986556899999999987554

iron dependent repressor

>COG3432 Predicted transcriptional regulator [Transcription]

Probab=82.43  E-value=1.3  Score=37.76  Aligned_cols=37  Identities=14%  Similarity=0.183  Sum_probs=30.1

Q ss_pred             hHHHHHhhcCCeEEEcCCC---eeecchhHHHHHHhhhcc
Q psy8714         509 PVHINNICQRNYVTVTSGR---RLVPTSLGIVLVHGYQKI  545 (562)
Q Consensus       509 a~iI~~L~~r~Yi~~~~~k---~l~~T~~G~~li~~l~~~  545 (562)
                      ..+|+-|.++|.+...+++   .+..|++|+.+++.+..+
T Consensus        49 ~~yi~~L~~~Gli~~~~~~~~~~y~lT~KG~~fle~y~~i   88 (95)
T COG3432          49 QKYIEMLVEKGLIIKQDNGRRKVYELTEKGKRFLEKYSEI   88 (95)
T ss_pred             HHHHHHHHhCCCEEeccCCccceEEEChhHHHHHHHHHHH
Confidence            4699999999977764443   699999999999988654

>TIGR01056 topB DNA topoisomerase III, bacteria and conjugative plasmid

Probab=81.59  E-value=4.2  Score=46.98  Aligned_cols=128  Identities=13%  Similarity=0.149  Sum_probs=75.5

Q ss_pred             HHHHHHHHHHHh--hcccCceEEEEEEEEEECCeEEEEEEEEEeecceeeeecccccccCCCCCCCCCCeeeeeeeEEee
Q psy8714         402 RLYDYIVRHFIG--TLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKMVE  479 (562)
Q Consensus       402 ~vY~lI~rr~la--~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~v~~~~~~~~~~Lp~l~~G~~~~~~~~~i~e  479 (562)
                      -.-.||+.|..+  .| .|..|=...+.+..++..|.+.-.......++ +...+.. +..+-.+ .|..+.|.++..++
T Consensus       200 ptL~lIveRe~eI~~F-~p~~y~~i~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~a-~~i~~~~-~~~~~~V~~v~~k~  275 (660)
T TIGR01056       200 PTLAMVVKRENEIKNF-VGKPFYEVSATINKDEQEFTTEWQPYKDEEER-ELHEFLA-ENVVTDL-TQKPALVTDIEKER  275 (660)
T ss_pred             hhhHHHHHHHHHHHcC-CCCccEEEEEEEEcCCceEEEEEeccCCcccC-cCCHHHH-HHHHHHh-hCCCeEEEEEEeee
Confidence            344567777665  44 34444455566655555666653211111111 1100000 1111122 23457788899999


Q ss_pred             eecCCCCCCCHHHHHHHHH-hcCCCCcCchhHHHHHhhcC-CeEEE-cCCCeeecchh
Q psy8714         480 RKTTPPDYLTESELISLME-KHGIGTDASIPVHINNICQR-NYVTV-TSGRRLVPTSL  534 (562)
Q Consensus       480 ~~TkPP~~~Te~~Li~~Me-~~GIGTpATra~iI~~L~~r-~Yi~~-~~~k~l~~T~~  534 (562)
                      ++..||++|+-++|...+- +.|+...-|. .|.+.|++. |||.- ......+|.+.
T Consensus       276 ~~~~pP~pf~ts~LQ~~as~~~g~s~~~tm-~iAQ~LYE~~glITYpRTDS~~ls~~~  332 (660)
T TIGR01056       276 KKTSAPLFYDLSALQEDANKRFGISAKRTL-DIAQKLYETHKLITYPRTDSRYLPEDE  332 (660)
T ss_pred             eecCCCCCCCHHHHHHHHHHhcCCCHHHHH-HHHHHHHHhCCEEEEecCCCccCCHHH
Confidence            9999999999999999885 4588666666 799999997 99973 12234455544

This model describes topoisomerase III from bacteria and its equivalents encoded on plasmids. The gene is designated topB if found in the bacterial chromosome, traE on conjugative plasmid RP4, etc. These enzymes are involved in the control of DNA topology. DNA topoisomerase III belongs to the type I topoisomerases, which are ATP-independent.

>PRK08173 DNA topoisomerase III; Validated

Probab=81.18  E-value=3.6  Score=48.95  Aligned_cols=110  Identities=18%  Similarity=0.328  Sum_probs=68.8

Q ss_pred             hhhhhhhhhhhcccC-cceEEEEEEEeeCCeEEEEEee----cc--cccCH--HHHHHHHHHhhhcCceEEEEEEcceee
Q psy8714         219 GFCVERHDKIRTFKP-EPYWLLDLTLNLNGVAVSVTWS----RG--HIFDK--STCNVFFKAVEKEKHVTVVDVQSSTKS  289 (562)
Q Consensus       219 ~lIv~Re~eI~~F~p-~~y~~i~~~~~~~~~~~~~~~~----~~--~~~~~--~~a~~~~~~~~~~~~~~V~~v~~~~~~  289 (562)
                      .||+.|..+.  |=| .-|=...+.+..++..|.+...    .|  .++..  +..+..+-.+.....+.+.+++..++.
T Consensus       406 ~lI~rRfla~--f~~~a~~~~t~v~~~v~~~~F~a~G~~~~~~Gw~~vy~~~~~~~~~~LP~l~~Ge~~~~~~~~~~e~~  483 (862)
T PRK08173        406 DLVVKRFLAV--FFPAAEFLVTTRITEVAGHHFKTEGKVLVNPGWLAVYGKEAQGADANLVPVQKGEKVKTDKIEAVALT  483 (862)
T ss_pred             HHHHHHHHHH--hCchheEEEEEEEEEeCCcEEEEEEEEEeeCChHHHhCcccccccccCCCcCCCCEeeeeeeeecccc
Confidence            5666666544  444 4444455666677777776532    11  11110  001111222333345777888889999


Q ss_pred             ccCCCCCCHHHHHHHHHh---------------hCCCC-HHHHHHHHHHhHhcCcee
Q psy8714         290 KTKPQALNTVELMRVASS---------------GLGMG-PHHAMQIAERLYTQGYVS  330 (562)
Q Consensus       290 ~~pP~pf~l~~Lq~~a~~---------------~~g~s-~~~tl~iaQ~LYE~glIS  330 (562)
                      +.||.+|+=++|...|-.               ..|+. |.-=-.|.+.|++.|||.
T Consensus       484 TkPP~ryTEatLl~aMe~~gk~v~D~el~~~~~~~GIGTpATRA~IIe~L~~r~Yi~  540 (862)
T PRK08173        484 TKPPARYNEATLLSAMEGAGKLVEDDELREAMAEKGLGTPATRAAIIEGLLGEKYLV  540 (862)
T ss_pred             cCCCCCcCHHHHHHHHHhhhhccccHHHHhhhhcCCCCchhhHHHHHHHHHhCCcEE
Confidence            999999999999988863               35665 444456799999999997

>PF08259 Periviscerokin: Periviscerokinin family; InterPro: IPR013231 Perviscerokinin neuropeptides are found in the abdominal perisympathetic organs of insects

Probab=80.79  E-value=0.69  Score=23.43  Aligned_cols=9  Identities=33%  Similarity=1.025  Sum_probs=7.9

Q ss_pred             cCceeecCC
Q psy8714         326 QGYVSYPRT  334 (562)
Q Consensus       326 ~glISYPRT  334 (562)
                      .|+|++|||
T Consensus         3 sGlI~fpR~   11 (11)
T PF08259_consen    3 SGLIPFPRV   11 (11)
T ss_pred             ccccccCCC
Confidence            489999997

They mediate visceral muscle contractile activity (myotropic activity). CAPA, which are in the periviscerokinin and pyrokinin peptide families, has potential medical importance. This is due to its myotropic effects on, for example, heart muscles and due to its occurrence in the Ixodoidea (ticks), which are important vectors in the transmission of many animal diseases []. These peptides also have a strong diuretic or anti-diuretic effect, suggesting they have significant medical implications [].

>PRK11512 DNA-binding transcriptional repressor MarR; Provisional

Probab=80.58  E-value=2.1  Score=39.14  Aligned_cols=50  Identities=12%  Similarity=0.205  Sum_probs=37.8

Q ss_pred             CCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEcC----C--CeeecchhHHHHHHh
Q psy8714         488 LTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTS----G--RRLVPTSLGIVLVHG  541 (562)
Q Consensus       488 ~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~~----~--k~l~~T~~G~~li~~  541 (562)
                      .|.++|-..|   |+ +++|-..+|+.|.++|||.+..    +  ..|.+|++|+.+++.
T Consensus        55 ~t~~eLa~~l---~i-~~~tvsr~l~~Le~~GlI~R~~~~~DrR~~~l~LT~~G~~~~~~  110 (144)
T PRK11512         55 ITPVELKKVL---SV-DLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTSGAAICEQ  110 (144)
T ss_pred             CCHHHHHHHH---CC-CHHHHHHHHHHHHHCCCEEeccCcccCCeeEeEEChhHHHHHHH
Confidence            4556665555   33 5788999999999999999731    1  359999999998755

>PRK14973 DNA topoisomerase I; Provisional

Probab=80.32  E-value=3.5  Score=49.36  Aligned_cols=110  Identities=14%  Similarity=0.264  Sum_probs=69.3

Q ss_pred             hhhhhhhhhhhcccCcceEEEEEEEeeCCeEEEEEee----cc--cccCH-HHHHHHHHHhhhcCceEEEEEEcceeecc
Q psy8714         219 GFCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWS----RG--HIFDK-STCNVFFKAVEKEKHVTVVDVQSSTKSKT  291 (562)
Q Consensus       219 ~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~----~~--~~~~~-~~a~~~~~~~~~~~~~~V~~v~~~~~~~~  291 (562)
                      .||+.|..+.. ..|.-|=+..+.+..++..|.+...    .|  .++.. +..+..+-.+.....+.+.+++..++.+.
T Consensus       385 ~LI~rRfLA~~-~~~a~~~~t~v~~~~~~~~F~a~G~~i~~~Gw~~vy~~~~~~~~~LP~l~~Ge~~~~~~~~~~e~~T~  463 (936)
T PRK14973        385 ELVVRRFLATL-SPDAEWATMKVNFDAGGEPYTATGGRLLEAGWRTVYPYSEAKENILPAFALGEKLPILAVNLEEKETQ  463 (936)
T ss_pred             HHHHHHHHHHh-ChhheEEEEEEEEEECCEEEEEEEEEEeecCeeEeecccccccccCCCccCCCEEEeeeeEEeecCCC
Confidence            46666665542 2445555666777766666765432    11  12110 11111222233334577778888899999


Q ss_pred             CCCCCCHHHHHHHHHhhCCCCHHH-HHHHHHHhHhcCcee
Q psy8714         292 KPQALNTVELMRVASSGLGMGPHH-AMQIAERLYTQGYVS  330 (562)
Q Consensus       292 pP~pf~l~~Lq~~a~~~~g~s~~~-tl~iaQ~LYE~glIS  330 (562)
                      ||..|+-++|.+.+-+ .|+.-.- =..|.+.|+++|||.
T Consensus       464 PP~ryTEatLik~ME~-~GIGTpATrA~II~~L~~R~Yve  502 (936)
T PRK14973        464 PPARYSQSRLIQRMEE-LGLGTKSTRHEVIGKLVSRKYIE  502 (936)
T ss_pred             CCCCCCHHHHHHHhcc-CCCCCcccHHHHHHHHHHccCee
Confidence            9999999999999854 5876444 456799999999993

>PRK05582 DNA topoisomerase I; Validated

Probab=80.32  E-value=4.8  Score=46.43  Aligned_cols=119  Identities=16%  Similarity=0.160  Sum_probs=73.1

Q ss_pred             HHHHHHHHHHHHHh--hcccCceEEEEEEEEEECCeEEEEEEEEEeecceeeeecccccccCCCCCCCCCCeeeeeeeEE
Q psy8714         400 AWRLYDYIVRHFIG--TLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKM  477 (562)
Q Consensus       400 e~~vY~lI~rr~la--~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~v~~~~~~~~~~Lp~l~~G~~~~~~~~~i  477 (562)
                      +--+-.+|+.|..+  .|-|..-| ...+.+..++..|.+.-.......++ ++..+.. +..+-.+. |..+.+.++..
T Consensus       168 QtPtL~lvv~Re~eI~~F~p~~y~-~i~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~a-~~~~~~~~-~~~~~v~~v~~  243 (650)
T PRK05582        168 QSVALKLIIDREKEIRAFVPEEYW-TIDAEFKKGKKKFEASFYGYKGKKIE-LKNEEDV-KEILAELK-KKDFKVSKVKK  243 (650)
T ss_pred             hHhHHHHHHhHHHHHHhCCCCccE-EEEEEEecCCccEEEEEEecCCCccc-cCCHHHH-HHHHHHhc-CCCeEEEEEee
Confidence            33445678888854  55544444 44455555555566543111111111 1111000 11111222 34567778899


Q ss_pred             eeeecCCCCCCCHHHHHHHHH-hcCCCCcCchhHHHHHhhc---------CCeEEE
Q psy8714         478 VERKTTPPDYLTESELISLME-KHGIGTDASIPVHINNICQ---------RNYVTV  523 (562)
Q Consensus       478 ~e~~TkPP~~~Te~~Li~~Me-~~GIGTpATra~iI~~L~~---------r~Yi~~  523 (562)
                      +++++.||.+|+-++|...|- +.|+...-|. .|.+.|++         .|||.-
T Consensus       244 ~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl-~~aQ~LYe~~~~~~~~~~gliSY  298 (650)
T PRK05582        244 KERKRNPPPPFTTSTLQQEAARKLNFSTKKTM-MIAQQLYEGIDLGKQGTVGLITY  298 (650)
T ss_pred             eeeecCCCCCccHHHHHHHHHHHcCCCHHHHH-HHHHHHhcccccCCCCceEEEEe
Confidence            999999999999999998774 5699888888 79999999         699973

>PF07848 PaaX: PaaX-like protein; InterPro: IPR012906 This entry describes the N-terminal region of proteins that are similar to, and nclude, the product of the paaX gene of Escherichia coli (P76086 from SWISSPROT)

Probab=80.31  E-value=1.6  Score=35.27  Aligned_cols=49  Identities=20%  Similarity=0.388  Sum_probs=36.6

Q ss_pred             CCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEcC-CC--eeecchhH
Q psy8714         486 DYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTS-GR--RLVPTSLG  535 (562)
Q Consensus       486 ~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~~-~k--~l~~T~~G  535 (562)
                      ....-++|+..|+..||+.+|+|.. +..|.++|.++..+ |+  .+.+|+.|
T Consensus        19 ~~i~~~~Li~ll~~~Gv~e~avR~a-lsRl~~~G~L~~~r~Gr~~~Y~Lt~~g   70 (70)
T PF07848_consen   19 GWIWVASLIRLLAAFGVSESAVRTA-LSRLVRRGWLESERRGRRSYYRLTERG   70 (70)
T ss_dssp             S-EEHHHHHHHHCCTT--HHHHHHH-HHHHHHTTSEEEECCCTEEEEEE-HHH
T ss_pred             CceeHHHHHHHHHHcCCChHHHHHH-HHHHHHcCceeeeecCccceEeeCCCC
Confidence            4456789999999999999999975 57999999999743 22  48888876

PaaX is a transcriptional regulator that is always found in association with operons believed to be involved in the degradation of phenylacetic acid []. The gene product has been shown to bind to the promoter sites and repress their transcription []. ; PDB: 3KFW_X 3L09_B.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	562
1ecl_A	597	Amino Terminal 67kda Domain Of Escherichia Coli Dna		6e-26
1cy1_A	599	Complex Of E.Coli Dna Topoisomerase I With 5'ptptpt		2e-25
3pwt_A	596	Crystal Structure Of Mutant E.Coli Topoisomerase Ia		1e-24
1mw8_X	592	Crystal Structure Of A Complex Between H365r Mutant		2e-24
3px7_A	595	Crystal Structure Of Covalent Complex Of Topoisomer		9e-24
2gai_A	633	Structure Of Full Length Topoisomerase I From Therm		5e-20
2o19_A	659	Structure Of E. Coli Topoisomersae Iii In Complex W		3e-17
1d6m_A	653	Crystal Structure Of E. Coli Dna Topoisomerase Iii		3e-17
1gku_B	1054	Reverse Gyrase From Archaeoglobus Fulgidus Length =		7e-17
1i7d_A	659	Noncovalent Complex Of E.Coli Dna Topoisomerase Iii		8e-17
1gl9_B	1054	Archaeoglobus Fulgidus Reverse Gyrase Complexed Wit		8e-17
4ddt_A	1104	Thermotoga Maritima Reverse Gyrase, C2 Form 2 Lengt		2e-09
1cy9_A	264	Crystal Structure Of The 30 Kda Fragment Of E. Coli		3e-09

>pdb|1ECL|A Chain A, Amino Terminal 67kda Domain Of Escherichia Coli Dna Topoisomerase I (Residues 2-590 Of Mature Protein) Cloning Artifact Adds Two Residues To The Amino-Terminus Which Were Not Observed In The Experimental Electron Density (Gly-2, Ser-1) Length = 597

Iteration: 1
 Score =  115 bits (288), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 120/471 (25%), Positives = 195/471 (41%), Gaps = 34/471 (7%)
Query: 93  KLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAIT 152
           K K+ + L   A+  + + L  D D+EGE I + + E +       S     R  F+ IT
Sbjct: 89  KEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARYS-----RVVFNEIT 143
Query: 153 DKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGP 212
              I+ A     + NI    +  AR+ +D  +G   +    K          A  +S G 
Sbjct: 144 KNAIRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVSPLLWKKI--------ARGLSAGR 195
Query: 213 CQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNL---NGVAVSVTWSRGHIF---DKSTCN 266
            Q+  +   VER  +I+ F PE +W +D +        +A+ VT      F   +K    
Sbjct: 196 VQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEALALQVTHQNDKPFRPVNKEQTQ 255
Query: 267 VFFKAVEKEKHVTVVDVQSSTKSKTKPQA-LNTVELMRVASSGLGMGPHHAMQIAERLYT 325
                +EK ++  +      T SK  P A   T  L + AS+ LG G    M +A+RLY 
Sbjct: 256 AAVSLLEKARYSVLEREDKPTTSK--PGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYE 313
Query: 326 QGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVGDHPPI 385
            GY++Y RT++T   +  D V ++R   S      ++ E  +   S   KG     H  I
Sbjct: 314 AGYITYMRTDSTNLSQ--DAVNMVRGYISDNFGKKYLPESPNQYAS---KGNSQEAHEAI 368
Query: 386 TPTKLATRTQ----LDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKY 441
            P+ +    +    ++ DA +LY  I R F+        Y          D       + 
Sbjct: 369 RPSDVNVMAESLKDMEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRI 428
Query: 442 LLHPGFTGVMTWSAMKNES--IPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEK 499
           L   G+T VM      +E   +P    GD + +  +   +  T PP   +E+ L+  +EK
Sbjct: 429 LRFDGWTKVMPALRKGDEDRILPAVNKGDALTLVELTPAQHFTKPPARFSEASLVKELEK 488
Query: 500 HGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELV 550
            GIG  ++    I+ I  R YV V + RR     +G ++    ++  REL+
Sbjct: 489 RGIGRPSTYASIISTIQDRGYVRVEN-RRFYAEKMGEIVTDRLEENFRELM 538

>pdb|1CY1|A Chain A, Complex Of E.Coli Dna Topoisomerase I With 5'ptptpt Length = 599

Iteration: 1
 Score =  113 bits (283), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 118/471 (25%), Positives = 195/471 (41%), Gaps = 34/471 (7%)
Query: 93  KLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAIT 152
           K K+ + L   A+  + + L  D D+EGE I + + E +       S     R  F+ IT
Sbjct: 91  KEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARYS-----RVVFNEIT 145
Query: 153 DKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGP 212
              I+ A     + NI    +  AR+ +D  +G   +    K          A  +S G 
Sbjct: 146 KNAIRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVSPLLWKKI--------ARGLSAGR 197
Query: 213 CQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNL---NGVAVSVTWSRGHIF---DKSTCN 266
            Q+  +   VER  +I+ F PE +W +D +        +A+ VT      F   +K    
Sbjct: 198 VQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEALALQVTHQNDKPFRPVNKEQTQ 257
Query: 267 VFFKAVEKEKHVTVVDVQSSTKSKTKPQA-LNTVELMRVASSGLGMGPHHAMQIAERLYT 325
                +EK ++  +      T SK  P A   T  L + AS+ LG G    M +A+RLY 
Sbjct: 258 AAVSLLEKARYSVLEREDKPTTSK--PGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYE 315
Query: 326 QGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVGDHPPI 385
            GY++Y RT++T   +  D V ++R    S ++G        N  +     ++   H  I
Sbjct: 316 AGYITYMRTDSTNLSQ--DAVNMVRGY-ISDNFGKKYLPESPNQYASKENSQEA--HEAI 370
Query: 386 TPTKLATRTQ----LDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKY 441
            P+ +    +    ++ DA +LY  I R F+        Y          D       + 
Sbjct: 371 RPSDVNVMAESLKDMEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRI 430
Query: 442 LLHPGFTGVMTWSAMKNES--IPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEK 499
           L   G+T VM      +E   +P    GD + +  +   +  T PP   +E+ L+  +EK
Sbjct: 431 LRFDGWTKVMPALRKGDEDRILPAVNKGDALTLVELTPAQHFTKPPARFSEASLVKELEK 490
Query: 500 HGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELV 550
            GIG  ++    I+ I  R YV V + RR     +G ++    ++  REL+
Sbjct: 491 RGIGRPSTYASIISTIQDRGYVRVEN-RRFYAEKMGEIVTDRLEENFRELM 540

>pdb|3PWT|A Chain A, Crystal Structure Of Mutant E.Coli Topoisomerase Ia Length = 596

Iteration: 1
 Score =  111 bits (278), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 117/471 (24%), Positives = 195/471 (41%), Gaps = 34/471 (7%)
Query: 93  KLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAIT 152
           K K+ + L   A+  + + L  + D+EGE I + + E +       S     R  F+ IT
Sbjct: 89  KEKVVSELKQLAEKADHIYLATNLDREGEAIAWHLREVIGGDDARYS-----RVVFNEIT 143
Query: 153 DKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGP 212
              I+ A     + NI    +  AR+ +D  +G   +    K          A  +S G 
Sbjct: 144 KNAIRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVSPLLWKKI--------ARGLSAGR 195
Query: 213 CQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNL---NGVAVSVTWSRGHIF---DKSTCN 266
            Q+  +   VER  +I+ F PE +W +D +        +A+ VT      F   +K    
Sbjct: 196 VQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEALALQVTHQNDKPFRPVNKEQTQ 255
Query: 267 VFFKAVEKEKHVTVVDVQSSTKSKTKPQA-LNTVELMRVASSGLGMGPHHAMQIAERLYT 325
                +EK ++  +      T SK  P A   T  L + AS+ LG G    M +A+RLY 
Sbjct: 256 AAVSLLEKARYSVLEREDKPTTSK--PGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYE 313
Query: 326 QGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVGDHPPI 385
            GY++Y RT++T   +  D V ++R    S ++G        N  +     ++   H  I
Sbjct: 314 AGYITYMRTDSTNLSQ--DAVNMVRGY-ISDNFGKKYLPESPNQYASKENSQEA--HEAI 368
Query: 386 TPTKLATRTQ----LDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKY 441
            P+ +    +    ++ DA +LY  I R F+        Y          D       + 
Sbjct: 369 RPSDVNVMAESLKDMEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRI 428
Query: 442 LLHPGFTGVMTWSAMKNES--IPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEK 499
           L   G+T VM      +E   +P    GD + +  +   +  T PP   +E+ L+  +EK
Sbjct: 429 LRFDGWTKVMPALRKGDEDRILPAVNKGDALTLVELTPAQHFTKPPARFSEASLVKELEK 488
Query: 500 HGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELV 550
            GIG  ++    I+ I  R YV V + RR     +G ++    ++  REL+
Sbjct: 489 RGIGRPSTYASIISTIQDRGYVRVEN-RRFYAEKMGEIVTDRLEENFRELM 538

>pdb|1MW8|X Chain X, Crystal Structure Of A Complex Between H365r Mutant Of 67 Kda N-Terminal Fragment Of E. Coli Dna Topoisomerase I And 5'-Acttcgggatg-3' Length = 592

Iteration: 1
 Score =  110 bits (274), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 117/471 (24%), Positives = 195/471 (41%), Gaps = 34/471 (7%)
Query: 93  KLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAIT 152
           K K+ + L   A+  + + L  D D+EGE I + + E +       S     R  F+ IT
Sbjct: 89  KEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARYS-----RVVFNEIT 143
Query: 153 DKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGP 212
              I+ A     + NI    +  AR+ +D  +G   +    K          A  +S G 
Sbjct: 144 KNAIRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVSPLLWKKI--------ARGLSAGR 195
Query: 213 CQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNL---NGVAVSVTWSRGHIF---DKSTCN 266
            Q+  +   VER  +I+ F PE +W +D +        +A+ VT      F   +K    
Sbjct: 196 VQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEALALQVTHQNDKPFRPVNKEQTQ 255
Query: 267 VFFKAVEKEKHVTVVDVQSSTKSKTKPQA-LNTVELMRVASSGLGMGPHHAMQIAERLYT 325
                +EK ++  +      T SK  P A   T  L + AS+ LG G    M +A+RLY 
Sbjct: 256 AAVSLLEKARYSVLEREDKPTTSK--PGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYE 313
Query: 326 QGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVGDHPPI 385
            GY++Y RT++T   +  D V ++R    S ++G        N  +     ++  +   I
Sbjct: 314 AGYITYMRTDSTNLSQ--DAVNMVRGY-ISDNFGKKYLPESPNQYASKENSQEARE--AI 368
Query: 386 TPTKLATRTQ----LDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKY 441
            P+ +    +    ++ DA +LY  I R F+        Y          D       + 
Sbjct: 369 RPSDVNVMAESLKDMEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRI 428
Query: 442 LLHPGFTGVMTWSAMKNES--IPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEK 499
           L   G+T VM      +E   +P    GD + +  +   +  T PP   +E+ L+  +EK
Sbjct: 429 LRFDGWTKVMPALRKGDEDRILPAVNKGDALTLVELTPAQHFTKPPARFSEASLVKELEK 488
Query: 500 HGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELV 550
            GIG  ++    I+ I  R YV V + RR     +G ++    ++  REL+
Sbjct: 489 RGIGRPSTYASIISTIQDRGYVRVEN-RRFYAEKMGEIVTDRLEENFRELM 538

>pdb|3PX7|A Chain A, Crystal Structure Of Covalent Complex Of Topoisomerase 1a With Substrate Length = 595

Iteration: 1
 Score =  108 bits (269), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 116/471 (24%), Positives = 194/471 (41%), Gaps = 34/471 (7%)
Query: 93  KLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAIT 152
           K K+ + L   A+  + + L  + D+EGE I + + E +       S     R  F+ IT
Sbjct: 89  KEKVVSELKQLAEKADHIYLATNLDREGEAIAWHLREVIGGDDARYS-----RVVFNEIT 143
Query: 153 DKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGP 212
              I+ A     + NI    +  AR+ +D  +G   +    K          A  +S G 
Sbjct: 144 KNAIRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVSPLLWKKI--------ARGLSAGR 195
Query: 213 CQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNL---NGVAVSVTWSRGHIF---DKSTCN 266
            Q+  +   VER  +I+ F PE +W +D +        +A+ VT      F   +K    
Sbjct: 196 VQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEALALQVTHQNDKPFRPVNKEQTQ 255
Query: 267 VFFKAVEKEKHVTVVDVQSSTKSKTKPQA-LNTVELMRVASSGLGMGPHHAMQIAERLYT 325
                +EK ++  +      T SK  P A   T  L + AS+ LG G    M +A+RLY 
Sbjct: 256 AAVSLLEKARYSVLEREDKPTTSK--PGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYE 313
Query: 326 QGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVGDHPPI 385
            GY++  RT++T   +  D V ++R    S ++G        N  +     ++   H  I
Sbjct: 314 AGYITXMRTDSTNLSQ--DAVNMVRGY-ISDNFGKKYLPESPNQYASKENSQEA--HEAI 368
Query: 386 TPTKLATRTQ----LDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKY 441
            P+ +    +    ++ DA +LY  I R F+        Y          D       + 
Sbjct: 369 RPSDVNVMAESLKDMEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRI 428
Query: 442 LLHPGFTGVMTWSAMKNES--IPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEK 499
           L   G+T VM      +E   +P    GD + +  +   +  T PP   +E+ L+  +EK
Sbjct: 429 LRFDGWTKVMPALRKGDEDRILPAVNKGDALTLVELTPAQHFTKPPARFSEASLVKELEK 488
Query: 500 HGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELV 550
            GIG  ++    I+ I  R YV V + RR     +G ++    ++  REL+
Sbjct: 489 RGIGRPSTYASIISTIQDRGYVRVEN-RRFYAEKMGEIVTDRLEENFRELM 538

>pdb|2GAI|A Chain A, Structure Of Full Length Topoisomerase I From Thermotoga Maritima In Triclinic Crystal Form Length = 633

Iteration: 1
 Score = 95.9 bits (237), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 112/468 (23%), Positives = 197/468 (42%), Gaps = 46/468 (9%)
Query: 93  KLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAIT 152
           K K+   L + AK  E L+   D D+EGE I + +          N+     R  FS IT
Sbjct: 63  KEKVVEKLKDLAKKGELLIAS-DMDREGEAIAWHIARVT------NTLGRKNRIVFSEIT 115
Query: 153 DKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGP 212
            + I+ A+ N  + ++ + R+  AR+ LD  +G + +    + F+        S +S G 
Sbjct: 116 PRVIREAVKNPREIDMKKVRAQLARRILDRIVGYSLSPVLWRNFK--------SNLSAGR 167
Query: 213 CQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAV 272
            Q+ TL    +R  +I  F P+ Y  +  T+N +G+   +       FD  T     K +
Sbjct: 168 VQSATLKLVCDREREILRFVPKKYHRI--TVNFDGLTAEIDVKEKKFFDAET----LKEI 221
Query: 273 EKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQ------ 326
           +    + V + + S K    P+   T  L + A S LG      M IA++LY        
Sbjct: 222 QSIDELVVEEKKVSVKKFAPPEPFKTSTLQQEAYSKLGFSVSKTMMIAQQLYEGVETKDG 281
Query: 327 --GYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVGD-HP 383
              +++Y RT++T+     D      +   +  +G+   E + +   + +    + D H 
Sbjct: 282 HIAFITYMRTDSTRVS---DYAKEEARNLITEVFGE---EYVGSKRERRKSNAKIQDAHE 335
Query: 384 PITPTKLATRTQ-----LDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTME 438
            I PT +    +     L+ D  +LY+ I + F+ +      Y +        D  +  +
Sbjct: 336 AIRPTNVFMTPEEAGKYLNSDQKKLYELIWKRFLASQMKPSQYEETRFVLRTKDGKYRFK 395
Query: 439 AKYL--LHPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISL 496
              L  +  G+  V  W   +N     F+ G+ +    VK+ E++T P    TE  L+  
Sbjct: 396 GTVLKKIFDGYEKV--WKTERNTGEFPFEEGESVKPVVVKIEEQETKPKPRYTEGSLVKE 453
Query: 497 MEKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQK 544
           ME+ GIG  ++    I  +  R Y+    G  L PT +G V++   +K
Sbjct: 454 MERLGIGRPSTYASTIKLLLNRGYIKKIRG-YLYPTIVGSVVMDYLEK 500

>pdb|2O19|A Chain A, Structure Of E. Coli Topoisomersae Iii In Complex With An 8- Base Single Stranded Oligonucleotide. Frozen In Glycerol At Ph 5.5 Length = 659

Iteration: 1
 Score = 87.0 bits (214), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 112/526 (21%), Positives = 210/526 (39%), Gaps = 70/526 (13%)
Query: 65  FTSKYNNWDKVD-PLELFSCPTEKREA-TPKLKLPAFLANEAKDCEFLVLWLDCDKEGEN 122
           + S+Y  W+  D P+       + R + T +L +     +EA +   +V   D D+EG+ 
Sbjct: 54  YDSRYARWNLADLPIVPEKWQLQPRPSVTKQLNVIKRFLHEASE---IVHAGDPDREGQL 110
Query: 123 ICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNLVKPNIFEARSVDA--RQEL 180
           +  EV++ +  Q+     + V R   + +  + ++ A+  L   + F    V A  R   
Sbjct: 111 LVDEVLDYL--QLAPEKRQQVQRCLINDLNPQAVERAIDRLRSNSEFVPLCVSALARARA 168
Query: 181 DLRIGCAFTRYQTKF-----FQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEP 235
           D   G   TR  T       +QG        ++S G  QTP LG  V R ++I  F  + 
Sbjct: 169 DWLYGINMTRAYTILGRNAGYQG--------VLSVGRVQTPVLGLVVRRDEEIENFVAKD 220
Query: 236 YWLLDL-TLNLNGVAVSVTWS-----------RGHIFDKSTCNVFFKAVEKEKHVTVVDV 283
           ++ +    +       +  W             G +  +         +  +  + V   
Sbjct: 221 FFEVKAHIVTPADERFTAIWQPSEACEPYQDEEGRLLHRPLAEHVVNRISGQPAI-VTSY 279
Query: 284 QSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLY-TQGYVSYPRTETTQYPE- 341
               +S++ P   +   L   A+   G+   + + I ++LY T   ++YPR++    PE 
Sbjct: 280 NDKRESESAPLPFSLSALQIEAAKRFGLSAQNVLDICQKLYETHKLITYPRSDCRYLPEE 339
Query: 342 NFDLVAVLRQQESSPDWGDHVREVLSNGISKPR------KGKDVGDHPPITPTKLATRTQ 395
           +F     +    S      H  ++L   +  P         K V  H  I PT  ++   
Sbjct: 340 HFAGRHAVMNAISV-----HAPDLLPQPVVDPDIRNRCWDDKKVDAHHAIIPTARSSAIN 394
Query: 396 LDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSA 455
           L  +  ++Y+ I R ++   C D V+ + V +  +A   F  +A++L   G+  ++    
Sbjct: 395 LTENEAKVYNLIARQYLMQFCPDAVFRKCVIELDIAKGKFVAKARFLAEAGWRTLLGSKE 454
Query: 456 MKNES----IPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLM-------------- 497
              E+    +P    GD +  +  ++VER+T PP + T++ L+S M              
Sbjct: 455 RDEENDGTPLPVVAKGDELLCEKGEVVERQTQPPRHFTDATLLSAMTGIARFVQDKDLKK 514
Query: 498 ---EKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVH 540
                 G+GT+A+    I  + +R ++T   GR +  T  G  L H
Sbjct: 515 ILRATDGLGTEATRAGIIELLFKRGFLT-KKGRYIHSTDAGKALFH 559

>pdb|1D6M|A Chain A, Crystal Structure Of E. Coli Dna Topoisomerase Iii Length = 653

Iteration: 1
 Score = 87.0 bits (214), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 112/526 (21%), Positives = 210/526 (39%), Gaps = 70/526 (13%)
Query: 65  FTSKYNNWDKVD-PLELFSCPTEKREA-TPKLKLPAFLANEAKDCEFLVLWLDCDKEGEN 122
           + S+Y  W+  D P+       + R + T +L +     +EA +   +V   D D+EG+ 
Sbjct: 54  YDSRYARWNLADLPIVPEKWQLQPRPSVTKQLNVIKRFLHEASE---IVHAGDPDREGQL 110
Query: 123 ICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNLVKPNIFEARSVDA--RQEL 180
           +  EV++ +  Q+     + V R   + +  + ++ A+  L   + F    V A  R   
Sbjct: 111 LVDEVLDYL--QLAPEKRQQVQRCLINDLNPQAVERAIDRLRSNSEFVPLCVSALARARA 168
Query: 181 DLRIGCAFTRYQTKF-----FQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEP 235
           D   G   TR  T       +QG        ++S G  QTP LG  V R ++I  F  + 
Sbjct: 169 DWLYGINMTRAYTILGRNAGYQG--------VLSVGRVQTPVLGLVVRRDEEIENFVAKD 220
Query: 236 YWLLDL-TLNLNGVAVSVTWS-----------RGHIFDKSTCNVFFKAVEKEKHVTVVDV 283
           ++ +    +       +  W             G +  +         +  +  + V   
Sbjct: 221 FFEVKAHIVTPADERFTAIWQPSEACEPYQDEEGRLLHRPLAEHVVNRISGQPAI-VTSY 279
Query: 284 QSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLY-TQGYVSYPRTETTQYPE- 341
               +S++ P   +   L   A+   G+   + + I ++LY T   ++YPR++    PE 
Sbjct: 280 NDKRESESAPLPFSLSALQIEAAKRFGLSAQNVLDICQKLYETHKLITYPRSDCRYLPEE 339
Query: 342 NFDLVAVLRQQESSPDWGDHVREVLSNGISKPR------KGKDVGDHPPITPTKLATRTQ 395
           +F     +    S      H  ++L   +  P         K V  H  I PT  ++   
Sbjct: 340 HFAGRHAVMNAISV-----HAPDLLPQPVVDPDIRNRCWDDKKVDAHHAIIPTARSSAIN 394
Query: 396 LDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSA 455
           L  +  ++Y+ I R ++   C D V+ + V +  +A   F  +A++L   G+  ++    
Sbjct: 395 LTENEAKVYNLIARQYLMQFCPDAVFRKCVIELDIAKGKFVAKARFLAEAGWRTLLGSKE 454
Query: 456 MKNES----IPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLM-------------- 497
              E+    +P    GD +  +  ++VER+T PP + T++ L+S M              
Sbjct: 455 RDEENDGTPLPVVAKGDELLCEKGEVVERQTQPPRHFTDATLLSAMTGIARFVQDKDLKK 514
Query: 498 ---EKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVH 540
                 G+GT+A+    I  + +R ++T   GR +  T  G  L H
Sbjct: 515 ILRATDGLGTEATRAGIIELLFKRGFLT-KKGRYIHSTDAGKALFH 559

>pdb|1GKU|B Chain B, Reverse Gyrase From Archaeoglobus Fulgidus Length = 1054

Iteration: 1
 Score = 85.5 bits (210), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 119/495 (24%), Positives = 203/495 (41%), Gaps = 104/495 (21%)
Query: 85   TEKREATPKL----------KLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQ 134
            TE RE+ PK           ++ A L   A D EF+++  D D EGE I +++       
Sbjct: 592  TEDRESCPKCGSENVDNSRSRIEA-LRKLAHDAEFVIVGTDPDTEGEKIAWDLKNL---- 646
Query: 135  ININSPKTVWRARFSAITDKDIKAAMWNL--VKPNIFEARSVDARQELDLRIGCAFTRYQ 192
              ++    V RA F  +T + I  A+ +L  V  N+ +A+ V  R+  D  IG   ++  
Sbjct: 647  --LSGCGAVKRAEFHEVTRRAILEALESLRDVDENLVKAQVV--RRIEDRWIGFVLSQKL 702
Query: 193  TKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSV 252
             + F  +        +S G  QT  LG+ ++R  + R                       
Sbjct: 703  WERFNNRN-------LSAGRAQTLVLGWIIDRFQESR----------------------- 732
Query: 253  TWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMG 312
               R  I      ++  +  E+E  +T+  V+   + +T      T  ++  A+  L   
Sbjct: 733  --ERRKIAIVRDFDLVLEHDEEEFDLTIKLVEEREELRTPLPPYTTETMLSDANRILKFS 790
Query: 313  PHHAMQIAERLYTQGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISK 372
                MQIA+ L+  G ++Y RT++T+       V+ + Q+ +    GD            
Sbjct: 791  VKQTMQIAQELFENGLITYHRTDSTR-------VSDVGQRIAKEYLGDDF---------V 834
Query: 373  PRKGKDVGDHPPITPTKLATRTQ-----------LDGDAWR---LYDYIVRHFIGTLCGD 418
             R+  + G H  I PT+  TR             ++G  W    LYD I R F+ + C  
Sbjct: 835  GREWGESGAHECIRPTRPLTRDDVQRLIQEGVLVVEGLRWEHFALYDLIFRRFMASQCRP 894
Query: 419  LVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSA--MKNESIPDFKPGDLIPIQSVK 476
              +   V K+S+  +  T E + ++         + A  +KNE          +P  + +
Sbjct: 895  --FKVVVKKYSIEFDGKTAEEERIVRAEGRAYELYRAVWVKNE----------LPTGTFR 942
Query: 477  MVERKTTPPDYL--TESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSL 534
            +     + P  L  T+SE+I +M++ GIG  ++    ++ +  RNYV    G R++PT L
Sbjct: 943  VKAEVKSVPKVLPFTQSEIIQMMKERGIGRPSTYATIVDRLFMRNYVVEKYG-RMIPTKL 1001
Query: 535  GI----VLVHGYQKI 545
            GI     LV  Y K 
Sbjct: 1002 GIDVFRFLVRRYAKF 1016

>pdb|1I7D|A Chain A, Noncovalent Complex Of E.Coli Dna Topoisomerase Iii With An 8-Base Single-Stranded Dna Oligonucleotide Length = 659

Iteration: 1
 Score = 85.5 bits (210), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 111/526 (21%), Positives = 210/526 (39%), Gaps = 70/526 (13%)
Query: 65  FTSKYNNWDKVD-PLELFSCPTEKREA-TPKLKLPAFLANEAKDCEFLVLWLDCDKEGEN 122
           + S+Y  W+  D P+       + R + T +L +     +EA +   +V   D D+EG+ 
Sbjct: 54  YDSRYARWNLADLPIVPEKWQLQPRPSVTKQLNVIKRFLHEASE---IVHAGDPDREGQL 110
Query: 123 ICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNLVKPNIFEARSVDA--RQEL 180
           +  EV++ +  Q+     + V R   + +  + ++ A+  L   + F    V A  R   
Sbjct: 111 LVDEVLDYL--QLAPEKRQQVQRCLINDLNPQAVERAIDRLRSNSEFVPLCVSALARARA 168
Query: 181 DLRIGCAFTRYQTKF-----FQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEP 235
           D   G   TR  T       +QG        ++S G  QTP LG  V R ++I  F  + 
Sbjct: 169 DWLYGINMTRAYTILGRNAGYQG--------VLSVGRVQTPVLGLVVRRDEEIENFVAKD 220
Query: 236 YWLLDL-TLNLNGVAVSVTWS-----------RGHIFDKSTCNVFFKAVEKEKHVTVVDV 283
           ++ +    +       +  W             G +  +         +  +  + V   
Sbjct: 221 FFEVKAHIVTPADERFTAIWQPSEACEPYQDEEGRLLHRPLAEHVVNRISGQPAI-VTSY 279
Query: 284 QSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLY-TQGYVSYPRTETTQYPE- 341
               +S++ P   +   L   A+   G+   + + I ++LY T   +++PR++    PE 
Sbjct: 280 NDKRESESAPLPFSLSALQIEAAKRFGLSAQNVLDICQKLYETHKLITFPRSDCRYLPEE 339
Query: 342 NFDLVAVLRQQESSPDWGDHVREVLSNGISKPR------KGKDVGDHPPITPTKLATRTQ 395
           +F     +    S      H  ++L   +  P         K V  H  I PT  ++   
Sbjct: 340 HFAGRHAVMNAISV-----HAPDLLPQPVVDPDIRNRCWDDKKVDAHHAIIPTARSSAIN 394
Query: 396 LDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSA 455
           L  +  ++Y+ I R ++   C D V+ + V +  +A   F  +A++L   G+  ++    
Sbjct: 395 LTENEAKVYNLIARQYLMQFCPDAVFRKCVIELDIAKGKFVAKARFLAEAGWRTLLGSKE 454
Query: 456 MKNES----IPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLM-------------- 497
              E+    +P    GD +  +  ++VER+T PP + T++ L+S M              
Sbjct: 455 RDEENDGTPLPVVAKGDELLCEKGEVVERQTQPPRHFTDATLLSAMTGIARFVQDKDLKK 514
Query: 498 ---EKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVH 540
                 G+GT+A+    I  + +R ++T   GR +  T  G  L H
Sbjct: 515 ILRATDGLGTEATRAGIIELLFKRGFLT-KKGRYIHSTDAGKALFH 559

>pdb|1GL9|B Chain B, Archaeoglobus Fulgidus Reverse Gyrase Complexed With Adpnp Length = 1054

Iteration: 1
 Score = 85.5 bits (210), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 118/497 (23%), Positives = 200/497 (40%), Gaps = 108/497 (21%)
Query: 85   TEKREATPKL----------KLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQ 134
            TE RE+ PK           ++ A L   A D EF+++  D D EGE I +++       
Sbjct: 592  TEDRESCPKCGSENVDNSRSRIEA-LRKLAHDAEFVIVGTDPDTEGEKIAWDLKNL---- 646
Query: 135  ININSPKTVWRARFSAITDKDIKAAMWNL--VKPNIFEARSVDARQELDLRIGCAFTRYQ 192
              ++    V RA F  +T + I  A+ +L  V  N+ +A+ V  R+  D  IG   ++  
Sbjct: 647  --LSGCGAVKRAEFHEVTRRAILEALESLRDVDENLVKAQVV--RRIEDRWIGFVLSQKL 702
Query: 193  TKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSV 252
             + F  +        +S G  QT  LG+ ++R  + R                       
Sbjct: 703  WERFNNRN-------LSAGRAQTLVLGWIIDRFQESR----------------------- 732
Query: 253  TWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMG 312
               R  I      ++  +  E+E  +T+  V+   + +T      T  ++  A+  L   
Sbjct: 733  --ERRKIAIVRDFDLVLEHDEEEFDLTIKLVEEREELRTPLPPYTTETMLSDANRILKFS 790
Query: 313  PHHAMQIAERLYTQGYVSYPRTETTQYPENFDLVA--VLRQQESSPDWGDHVREVLSNGI 370
                MQIA+ L+  G ++Y RT++T+  +    +A   L       +WG+          
Sbjct: 791  VKQTMQIAQELFENGLITYHRTDSTRVSDVGQRIAKEYLGDDFVGREWGES--------- 841
Query: 371  SKPRKGKDVGDHPPITPTKLATRTQ-----------LDGDAWR---LYDYIVRHFIGTLC 416
                     G H  I PT+  TR             ++G  W    LYD I R F+ + C
Sbjct: 842  ---------GAHECIRPTRPLTRDDVQRLIQEGVLVVEGLRWEHFALYDLIFRRFMASQC 892
Query: 417  GDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSA--MKNESIPDFKPGDLIPIQS 474
                +   V K+S+  +  T E + ++         + A  +KNE          +P  +
Sbjct: 893  RP--FKVVVKKYSIEFDGKTAEEERIVRAEGRAYELYRAVWVKNE----------LPTGT 940
Query: 475  VKMVERKTTPPDYL--TESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPT 532
             ++     + P  L  T+SE+I +M++ GIG  ++    ++ +  RNYV    G R++PT
Sbjct: 941  FRVKAEVKSVPKVLPFTQSEIIQMMKERGIGRPSTYATIVDRLFMRNYVVEKYG-RMIPT 999
Query: 533  SLGI----VLVHGYQKI 545
             LGI     LV  Y K 
Sbjct: 1000 KLGIDVFRFLVRRYAKF 1016

>pdb|4DDT|A Chain A, Thermotoga Maritima Reverse Gyrase, C2 Form 2 Length = 1104

Iteration: 1
 Score = 61.2 bits (147), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 104/472 (22%), Positives = 187/472 (39%), Gaps = 82/472 (17%)
Query: 106  DCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAM----- 160
            + + +++  D D EGE I ++V      Q  + S +++ R     IT    K A      
Sbjct: 659  EADEILVATDPDVEGEKISWDVT-----QYLLPSTRSLRRIEMHEITRYGFKKARESVRF 713
Query: 161  --WNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTL 218
              +NLVK  I        R+  D  IG   +       Q ++G    S +S G  Q+  L
Sbjct: 714  VDFNLVKAQI-------VRRVQDRWIGFELSGK----LQKRFG---RSNLSAGRVQSTVL 759
Query: 219  GFCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHV 278
            G+ VER ++ +  + + + LL L    NGV + V    G I D                V
Sbjct: 760  GWIVEREEEYKKSEKD-FTLLVLE---NGVNLEV---EGKIADDV--------------V 798
Query: 279  TVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQ 338
            TVV++Q + + K       T   +   S  L +G    M I + L+ +G+++Y RT++T+
Sbjct: 799  TVVELQEAEEEKNPLPPYTTSSALSEISQKLRLGVQEVMDILQDLFEKGFITYHRTDSTR 858
Query: 339  YPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVGDHPPITPTKLATRTQLD- 397
                   VA             ++R++    I   R     G H  I P K     +L+ 
Sbjct: 859  ISLEGQNVA-----------RTYLRKIGKEDIFMGRSWSTEGAHEAIRPVKPIDARELEE 907
Query: 398  -----------GDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKY-LLHP 445
                           R+Y+ I   F+ +    +   +++    V  +   +E    +L  
Sbjct: 908  MIEEGLIADLTKKHLRVYELIFNRFLASQSAAVKVKKQIVTVDVDGKRMGIEQIVEILRD 967
Query: 446  GFTGVMTWSAMKNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTD 505
            G+   +  +       P F+       +     +  T P    T++ ++  M+K GIG  
Sbjct: 968  GWNLFVPLTVS-----PRFEHRTYKIKEKKFYKKH-TVP--LFTQASIVEEMKKRGIGRP 1019
Query: 506  ASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGY--QKIDRELVEPTMR 555
            ++    +  + +R YV     +R+ PT  G V+V+ Y  ++ ++ + E T R
Sbjct: 1020 STYAKIVEVLFRRGYVYEDKYKRVRPTRFG-VMVYSYLKERYEKYVTEETTR 1070

>pdb|1CY9|A Chain A, Crystal Structure Of The 30 Kda Fragment Of E. Coli Dna Topoisomerase I. Monoclinic Form Length = 264

Iteration: 1
 Score = 60.5 bits (145), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 66/268 (24%), Positives = 107/268 (39%), Gaps = 20/268 (7%)
Query: 231 FKPEPYWLLDL---TLNLNGVAVSVTWSRGHIF---DKSTCNVFFKAVEKEKHVTVVDVQ 284
           F PE +W +D    T +   +A+ VT      F   +K         +EK ++  +    
Sbjct: 1   FVPEEFWEVDASTTTPSGEALALQVTHQNDKPFRPVNKEQTQAAVSLLEKARYSVLERED 60
Query: 285 SSTKSKTKPQA-LNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENF 343
             T SK  P A   T  L + AS+ LG G    M +A+RLY  GY++Y RT++T   +  
Sbjct: 61  KPTTSK--PGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYITYMRTDSTNLSQ-- 116
Query: 344 DLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVGDHPPITPTKLATRTQ----LDGD 399
           D V ++R   S  ++G        N  +     ++   H  I P+ +    +    ++ D
Sbjct: 117 DAVNMVRGYISD-NFGKKYLPESPNQYASKENSQEA--HEAIRPSDVNVMAESLKDMEAD 173
Query: 400 AWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNE 459
           A +LY  I R F+        Y          D       + L   G+T VM      +E
Sbjct: 174 AQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKGDE 233
Query: 460 S--IPDFKPGDLIPIQSVKMVERKTTPP 485
              +P    GD + +  +   +  T PP
Sbjct: 234 DRILPAVNKGDALTLVELTPAQHFTKPP 261

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	562
1i7d_A	659	DNA topoisomerase III; decatenating enzyme, protei	2e-61
2gai_A	633	DNA topoisomerase I; zinc ribbon; HET: DNA; 1.70A	3e-37
1mw9_X	592	DNA topoisomerase I; decatenase enzyme, toprim dom	1e-34
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	8e-34
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-08

>1i7d_A DNA topoisomerase III; decatenating enzyme, protein-DNA complex, single-stranded DNA, isomerase/DNA complex; HET: DNA; 2.05A {Escherichia coli} SCOP: e.10.1.1 PDB: 2o5c_A* 2o54_A* 2o59_A* 2o19_A* 2o5e_A* 1d6m_A* Length = 659

 Score =  213 bits (545), Expect = 2e-61
 Identities = 95/500 (19%), Positives = 183/500 (36%), Gaps = 72/500 (14%)

Query: 105 KDCEFLVLWLDCDKEGENICFEVMEAVRHQININSP-KTVWRARFSAITDKDIKAAMWNL 163
            +   +V   D D+EG+ +  EV++ ++         +       + +  + ++ A+  L
Sbjct: 93  HEASEIVHAGDPDREGQLLVDEVLDYLQLAPEKRQQVQRCL---INDLNPQAVERAIDRL 149

Query: 164 VKPNI-FE--ARSVDARQELDLRIGCAFTRYQT-KFFQGKYGDLDASLISYGPCQTPTLG 219
            + N  F     S  AR   D   G   TR  T       Y  +    +S G  QTP LG
Sbjct: 150 -RSNSEFVPLCVSALARARADWLYGINMTRAYTILGRNAGYQGV----LSVGRVQTPVLG 204

Query: 220 FCVERHDKIRTFKPEPYWLLDLTLNL-NGVAVSVTW-----------SRGHIFDKSTCNV 267
             V R ++I  F  + ++ +   +        +  W             G +  +     
Sbjct: 205 LVVRRDEEIENFVAKDFFEVKAHIVTPADERFTAIWQPSEACEPYQDEEGRLLHRPLAEH 264

Query: 268 FFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLY-TQ 326
               +   +   V       +S++ P   +   L   A+   G+   + + I ++LY T 
Sbjct: 265 VVNRI-SGQPAIVTSYNDKRESESAPLPFSLSALQIEAAKRFGLSAQNVLDICQKLYETH 323

Query: 327 GYVSYPRTETT-----QYPENFDLVAVLRQQESSPDWGDHVREVLSNGI---SKPRKGKD 378
             +++PR++        +     ++  +            V   + N      K      
Sbjct: 324 KLITFPRSDCRYLPEEHFAGRHAVMNAISVHAPDLLPQPVVDPDIRNRCWDDKK------ 377

Query: 379 VGDHPPITPTKLATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTME 438
           V  H  I PT  ++   L  +  ++Y+ I R ++   C D V+ + V +  +A   F  +
Sbjct: 378 VDAHHAIIPTARSSAINLTENEAKVYNLIARQYLMQFCPDAVFRKCVIELDIAKGKFVAK 437

Query: 439 AKYLLHPGFTGVMTWSAMKNE----SIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELI 494
           A++L   G+  ++       E     +P    GD +  +  ++VER+T PP + T++ L+
Sbjct: 438 ARFLAEAGWRTLLGSKERDEENDGTPLPVVAKGDELLCEKGEVVERQTQPPRHFTDATLL 497

Query: 495 SLME-----------------KHGIGTDA---SIPVHINNICQRNYVTVTSGRRLVPTSL 534
           S M                    G+GT+A    I   I  + +R ++T   GR +  T  
Sbjct: 498 SAMTGIARFVQDKDLKKILRATDGLGTEATRAGI---IELLFKRGFLTK-KGRYIHSTDA 553

Query: 535 GIVLVHGYQKIDRELVEPTM 554
           G  L   +  +      P M
Sbjct: 554 GKAL---FHSLPEMATRPDM 570

>2gai_A DNA topoisomerase I; zinc ribbon; HET: DNA; 1.70A {Thermotoga maritima} PDB: 2gaj_A* Length = 633

 Score =  145 bits (368), Expect = 3e-37
 Identities = 113/483 (23%), Positives = 178/483 (36%), Gaps = 104/483 (21%)

Query: 100 LANEAKDCEFLVLWL--DCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIK 157
           L + AK  E   L +  D D+EGE I + +          N+     R  FS IT + I+
Sbjct: 70  LKDLAKKGE---LLIASDMDREGEAIAWHIARV------TNTLGRKNRIVFSEITPRVIR 120

Query: 158 AAMWNLVKPNIFEARSVD--------ARQELDLRIGCAFTRYQ------TKFFQGKYGDL 203
            A+ N         R +D        AR+ LD  +G     Y         F        
Sbjct: 121 EAVKN--------PREIDMKKVRAQLARRILDRIVG-----YSLSPVLWRNFKSNL---- 163

Query: 204 DASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKS 263
                S G  Q+ TL    +R  +I  F P+ Y    +T+N +G+   +       FD  
Sbjct: 164 -----SAGRVQSATLKLVCDREREILRFVPKKYH--RITVNFDGLTAEIDVKEKKFFDAE 216

Query: 264 TCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERL 323
           T     K ++    + V + + S K    P+   T  L + A S LG      M IA++L
Sbjct: 217 T----LKEIQSIDELVVEEKKVSVKKFAPPEPFKTSTLQQEAYSKLGFSVSKTMMIAQQL 272

Query: 324 Y--------TQGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGI----- 370
           Y           +++Y RT++T+                S    +  R +++        
Sbjct: 273 YEGVETKDGHIAFITYMRTDSTRV---------------SDYAKEEARNLITEVFGEEYV 317

Query: 371 -SKPRKGKDVGD----HPPITPTKLATRT------QLDGDAWRLYDYIVRHFIGTLCGDL 419
            SK  + K        H  I PT +   T       L+ D  +LY+ I + F+ +     
Sbjct: 318 GSKRERRKSNAKIQDAHEAIRPTNV-FMTPEEAGKYLNSDQKKLYELIWKRFLASQMKPS 376

Query: 420 VYTQKVAKFSVADEMFTMEAKY--LLHPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKM 477
            Y +        D  +  +      +  G+  V  W   +N     F+ G+ +    VK+
Sbjct: 377 QYEETRFVLRTKDGKYRFKGTVLKKIFDGYEKV--WKTERNTGEFPFEEGESVKPVVVKI 434

Query: 478 VERKTTPPDYLTESELISLMEKHGIG---TDASIPVHINNICQRNYVTVTSGRRLVPTSL 534
            E++T P    TE  L+  ME+ GIG   T AS    I  +  R Y+       L PT +
Sbjct: 435 EEQETKPKPRYTEGSLVKEMERLGIGRPSTYAST---IKLLLNRGYIKK-IRGYLYPTIV 490

Query: 535 GIV 537
           G V
Sbjct: 491 GSV 493

>1mw9_X DNA topoisomerase I; decatenase enzyme, toprim domain; HET: DNA; 1.67A {Escherichia coli} SCOP: e.10.1.1 PDB: 1mw8_X* 1cy1_A* 1cy0_A* 1cy2_A* 1cy4_A* 1cy6_A* 1cy7_A* 1cy8_A* 3pwt_A* 3px7_A* 1ecl_A 1cy9_A* 1cyy_A* Length = 592

 Score =  136 bits (346), Expect = 1e-34
 Identities = 113/479 (23%), Positives = 180/479 (37%), Gaps = 90/479 (18%)

Query: 100 LANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAA 159
           L   A+  + + L  D D+EGE I + + E     I  +      R  F+ IT   I+ A
Sbjct: 96  LKQLAEKADHIYLATDLDREGEAIAWHLREV----IGGD-DARYSRVVFNEITKNAIRQA 150

Query: 160 MWNLVKPNIFEARSVD--------ARQELDLRIGCAFTRYQ------TKFFQGKYGDLDA 205
                         ++        AR+ +D  +G     Y        K  +G       
Sbjct: 151 FNK--------PGELNIDRVNAQQARRFMDRVVG-----YMVSPLLWKKIARGL------ 191

Query: 206 SLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNG---VAVSVTWSRG---HI 259
              S G  Q+  +   VER  +I+ F PE +W +D +        +A+ VT         
Sbjct: 192 ---SAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEALALQVTHQNDKPFRP 248

Query: 260 FDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQA-LNTVELMRVASSGLGMGPHHAMQ 318
            +K         +EK ++ +V++ +    +  KP A   T  L + AS+ LG G    M 
Sbjct: 249 VNKEQTQAAVSLLEKARY-SVLEREDKPTTS-KPGAPFITSTLQQAASTRLGFGVKKTMM 306

Query: 319 IAERLYTQGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGI------SK 372
           +A+RLY  GY++Y RT++T                 S D  + VR  +S+          
Sbjct: 307 MAQRLYEAGYITYMRTDSTNL---------------SQDAVNMVRGYISDNFGKKYLPES 351

Query: 373 PRKGKDVGD----HPPITPTKLATRT-----QLDGDAWRLYDYIVRHFIGTLCGDLVYTQ 423
           P +     +       I P+ +          ++ DA +LY  I R F+        Y  
Sbjct: 352 PNQYASKENSQEAREAIRPSDV-NVMAESLKDMEADAQKLYQLIWRQFVACQMTPAKYDS 410

Query: 424 KVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNES--IPDFKPGDLIPIQSVKMVERK 481
                   D       + L   G+T VM      +E   +P    GD + +  +   +  
Sbjct: 411 TTLTVGAGDFRLKARGRILRFDGWTKVMPALRKGDEDRILPAVNKGDALTLVELTPAQHF 470

Query: 482 TTPPDYLTESELISLMEKHGIG---TDASIPVHINNICQRNYVTVTSGRRLVPTSLGIV 537
           T PP   +E+ L+  +EK GIG   T ASI   I+ I  R YV V   RR     +G +
Sbjct: 471 TKPPARFSEASLVKELEKRGIGRPSTYASI---ISTIQDRGYVRVE-NRRFYAEKMGEI 525

>1gku_B Reverse gyrase, TOP-RG; topoisomerase, DNA supercoiling, archaea, helicase; 2.7A {Archaeoglobus fulgidus} SCOP: c.37.1.16 c.37.1.16 e.10.1.1 PDB: 1gl9_B* Length = 1054

 Score =  136 bits (344), Expect = 8e-34
 Identities = 101/534 (18%), Positives = 177/534 (33%), Gaps = 121/534 (22%)

Query: 50   LFKMTSVCGHI---------MGLD----FTSKYNNWDKVDPL------ELFSCPTEKREA 90
            +  +T+  GH+          G+     F   Y +  +          +  SCP    E 
Sbjct: 546  VLMVTASIGHVVDLITNRGFHGVLVNGRFVPVYASIKRCRDCGYQFTEDRESCPKCGSEN 605

Query: 91   TP-KLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFS 149
                      L   A D EF+++  D D EGE I +++         ++    V RA F 
Sbjct: 606  VDNSRSRIEALRKLAHDAEFVIVGTDPDTEGEKIAWDLKNL------LSGCGAVKRAEFH 659

Query: 150  AITDKDIKAAMWNLVKPNIFEARSVDA---RQELDLRIGCAFT---RYQTKFFQGKYGDL 203
             +T + I  A+ +       +   V A   R+  D  IG  F    +   +F        
Sbjct: 660  EVTRRAILEALES---LRDVDENLVKAQVVRRIEDRWIG--FVLSQKLWERF--NNRN-- 710

Query: 204  DASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKS 263
                +S G  QT  LG+ ++R  + R  +                               
Sbjct: 711  ----LSAGRAQTLVLGWIIDRFQESRERRKIAIV-------------------------R 741

Query: 264  TCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERL 323
              ++  +  E+E  +T+  V+   + +T      T  ++  A+  L       MQIA+ L
Sbjct: 742  DFDLVLEHDEEEFDLTIKLVEEREELRTPLPPYTTETMLSDANRILKFSVKQTMQIAQEL 801

Query: 324  YTQGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGK------ 377
            +  G ++Y RT++T+                S       +E L +       G+      
Sbjct: 802  FENGLITYHRTDSTRV---------------SDVGQRIAKEYLGDDFVGREWGESGAHEC 846

Query: 378  ----DVGDHP---PITPTKLATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSV 430
                          +    +     L  + + LYD I R F+ + C       K      
Sbjct: 847  IRPTRPLTRDDVQRLIQEGVLVVEGLRWEHFALYDLIFRRFMASQCRPFKVVVKKYSIEF 906

Query: 431  ADEM----FTMEAKYLLHPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKMVERKTTPPD 486
              +       + A+   +  +  V          +P            VK   +      
Sbjct: 907  DGKTAEEERIVRAEGRAYELYRAVW-----VKNELPTGTFR-------VKAEVKSVPKVL 954

Query: 487  YLTESELISLMEKHGIG---TDASIPVHINNICQRNYVTVTSGRRLVPTSLGIV 537
              T+SE+I +M++ GIG   T A+I   ++ +  RNYV      R++PT LGI 
Sbjct: 955  PFTQSEIIQMMKERGIGRPSTYATI---VDRLFMRNYVVE-KYGRMIPTKLGID 1004

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 56.0 bits (134), Expect = 2e-08
 Identities = 85/577 (14%), Positives = 162/577 (28%), Gaps = 196/577 (33%)

Query: 64  DFTSKYNNWDKVD-PLELFSCPTEKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGEN 122
            F   ++  D  D P  + S    K E    +        +A      + W    K  E 
Sbjct: 28  AFVDNFDCKDVQDMPKSILS----KEEIDHIIMSK-----DAVSGTLRLFWTLLSK-QEE 77

Query: 123 ICFEVMEAVRHQININSPKTVWRARF---SAITDKDIKA--AMWNLVKPNIFEARSVDAR 177
           +  + +E V  +IN     +  +      S +T   I+    ++N  +   F   +V +R
Sbjct: 78  MVQKFVEEV-LRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQV--FAKYNV-SR 133

Query: 178 QE--LDLR-------------------IG--------CAFTRYQTKFFQGKYGDLDASLI 208
            +  L LR                    G        C   + Q K     +       +
Sbjct: 134 LQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIF------WL 187

Query: 209 SYGPCQTPTL------GFCV-------ERHDKI---------------RTFKPEPYW--L 238
           +   C +P                    R D                 R  K +PY   L
Sbjct: 188 NLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCL 247

Query: 239 LDLTLNLNGVAVSVTWSRGHI--FD---------KSTCNVFFKAVEKEKHVTVVDVQSS- 286
           L L      V      +      F+         +      F +     H+++     + 
Sbjct: 248 LVL----LNV-----QNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTL 298

Query: 287 TKSKTKP---QALNTV--ELMRVASSGLGMGPHHAMQIAERL--------YTQGYVSYPR 333
           T  + K    + L+    +L R   +     P     IAE +          + +V+  +
Sbjct: 299 TPDEVKSLLLKYLDCRPQDLPREVLTT---NPRRLSIIAESIRDGLATWDNWK-HVNCDK 354

Query: 334 TETT-------QYP----ENFDLVAVLRQQESSPD------WGDHVREVLSNGISKPRKG 376
             T          P    + FD ++V       P       W D ++  +   ++K  K 
Sbjct: 355 LTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKY 414

Query: 377 KDVGDHPP-----ITPTKLATRTQLDG------------------DAWRL---------Y 404
             V   P      I    L  + +L+                   D+  L         Y
Sbjct: 415 SLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFY 474

Query: 405 DYIVRHFIGTLCGDLVYTQKVAKFSVA--DEMFTMEAKYLLHPGFTGVMTWSAMKNESIP 462
            +I  H          + +++  F +   D  F +E K               ++++S  
Sbjct: 475 SHIGHHLKNIE-----HPERMTLFRMVFLDFRF-LEQK---------------IRHDSTA 513

Query: 463 DFKPGDLIP-IQSVKMVERKTTPPDYLTESELISLME 498
               G ++  +Q +K  +      D   E  + ++++
Sbjct: 514 WNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILD 550

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	562
1i7d_A	659	DNA topoisomerase III; decatenating enzyme, protei	100.0
1mw9_X	592	DNA topoisomerase I; decatenase enzyme, toprim dom	100.0
2gai_A	633	DNA topoisomerase I; zinc ribbon; HET: DNA; 1.70A	100.0
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	100.0
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	100.0
1vdd_A	228	Recombination protein RECR; helix-hairpin-helix, z	94.44
2fcj_A	119	Small toprim domain protein; structural genomics,	92.78
1tbx_A	99	ORF F-93, hypothetical 11.0 kDa protein; sulfolobu	90.07
1t6t_1	118	Putative protein; structural genomics, PSI, protei	87.71
3vdp_A	212	Recombination protein RECR; zinc finger, DNA repai	87.0
1r7j_A	95	Conserved hypothetical protein SSO10A; winged heli	84.52

>1i7d_A DNA topoisomerase III; decatenating enzyme, protein-DNA complex, single-stranded DNA, isomerase/DNA complex; HET: DNA; 2.05A {Escherichia coli} SCOP: e.10.1.1 PDB: 2o5c_A* 2o54_A* 2o59_A* 2o19_A* 2o5e_A* 1d6m_A*

Probab=100.00  E-value=1.4e-131  Score=1105.99  Aligned_cols=531  Identities=21%  Similarity=0.339  Sum_probs=451.4

Q ss_pred             eEEEEecccCcCCcchHHhhcccccCCCCceeeeeeeeEc-CCCcEEEEEEeccccccccccc----CCCCCccCCCCCC
Q psy8714           6 KKLVPASEIKLARPSLISLLTPLQRMNGACSVHEWVGPLF-GDLVLFKMTSVCGHIMGLDFTS----KYNNWDKVDPLEL   80 (562)
Q Consensus         6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~~~~~~~~~g~~~-g~~~~~~Vt~~~GHl~~l~~~~----~y~~W~~~~p~~~   80 (562)
                      |+||||||     ||+|+.|++.+|...    ..-+||++ |++  |+||||+|||++|.+|+    +|+.|..+++ ++
T Consensus         1 M~LiIaEK-----Ps~Ak~Ia~~L~g~~----~r~~gy~e~g~~--~~Vt~~~GHl~~L~~p~~y~~~~k~W~~~~l-pi   68 (659)
T 1i7d_A            1 MRLFIAEK-----PSLARAIADVLPKPH----RKGDGFIECGNG--QVVTWCIGHLLEQAQPDAYDSRYARWNLADL-PI   68 (659)
T ss_dssp             CEEEEESS-----HHHHHHHHTTSCSCC----EEETTEEEETTT--EEEEECSSCSEEECCHHHHCGGGGSCCSTTC-SC
T ss_pred             CEEEEEEC-----HHHHHHHHHHhcCCc----ccCCCcEeeCCC--EEEEeccchhhcCCCccccchhccccccCCc-cc
Confidence            68999999     999999999995322    23478999 875  79999999999997654    4668886552 23


Q ss_pred             CCCCcccccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHHHH
Q psy8714          81 FSCPTEKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAM  160 (562)
Q Consensus        81 ~~~~~~~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~A~  160 (562)
                      ++..........+.++++.|++++++||+||||||||||||+|||||+++++...  +.++||+|+|||++|+++|++||
T Consensus        69 ~p~~~~~~v~~~~~~~~~~lk~l~k~ad~iiiAtD~DREGE~I~~~i~~~~~~~~--~~~~~v~R~~fs~iT~~aI~~A~  146 (659)
T 1i7d_A           69 VPEKWQLQPRPSVTKQLNVIKRFLHEASEIVHAGDPDREGQLLVDEVLDYLQLAP--EKRQQVQRCLINDLNPQAVERAI  146 (659)
T ss_dssp             CCSSCCEEECGGGHHHHHHHHHHHHHCSEEEEECCSSHHHHHHHHHHHHHTTCCH--HHHHTCEECCCSCCSHHHHHHHH
T ss_pred             ccccceeeecccHHHHHHHHHHHHhcCCeEEEcCCCCCCCCHHHHHHHHHhCccc--cCCCceEEEEEccCCHHHHHHHH
Confidence            2211111111223467888888889999999999999999999999999995200  00579999999999999999999


Q ss_pred             HhCCCCh--HhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhhhhhhhhhhcccCcceEE
Q psy8714         161 WNLVKPN--IFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWL  238 (562)
Q Consensus       161 ~nl~~~~--~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lIv~Re~eI~~F~p~~y~~  238 (562)
                      +||++++  .++++||+||+++|||||||+||++|+.+++...   ++.+|+||||||||+|||+||+||++|+|++||+
T Consensus       147 ~nlr~~~~~~~l~~A~~aR~~~D~lvG~n~Sr~lt~~~r~~~~---~~~lS~GRVQTPtL~lIv~Re~eI~~F~p~~yw~  223 (659)
T 1i7d_A          147 DRLRSNSEFVPLCVSALARARADWLYGINMTRAYTILGRNAGY---QGVLSVGRVQTPVLGLVVRRDEEIENFVAKDFFE  223 (659)
T ss_dssp             TTCEEGGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTC---CSCCCCCTTHHHHHHHHHHHHHHHHTCCCCEEEE
T ss_pred             hCCCCcchhhhHHHHHHHHHHHHHHHHHHhHHHHHHHHhhcCC---CCceecCccccchHHHHHHHHHHHHhCCCcceEE
Confidence            9999987  6899999999999999999999999998764321   2479999999999999999999999999999999


Q ss_pred             EEEEE-eeCCeEEEEEee-----------cccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHHHHHHHHH
Q psy8714         239 LDLTL-NLNGVAVSVTWS-----------RGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVAS  306 (562)
Q Consensus       239 i~~~~-~~~~~~~~~~~~-----------~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~  306 (562)
                      |.+.+ ..+++.|.+.|.           +++++|++.|+.+++.|.+ ..++|++|+.++++++||+||||++||++||
T Consensus       224 i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~a~~~~~~~~~-~~~~V~~v~~k~~~~~pP~pf~ts~LQ~~As  302 (659)
T 1i7d_A          224 VKAHIVTPADERFTAIWQPSEACEPYQDEEGRLLHRPLAEHVVNRISG-QPAIVTSYNDKRESESAPLPFSLSALQIEAA  302 (659)
T ss_dssp             EEEEEECTTCCEEEEEECCCGGGTTTBCTTCCBCCHHHHHHHHHHHSS-CEEECCEEEEEEEEECCCCSBCHHHHHHHHH
T ss_pred             EEEEEecCCCcEEEEEEEeccccccccccccccCCHHHHHHHHHHhcc-CCeEEEEEEeEEEEecCCCCccHHHHHHHHH
Confidence            99999 556677999993           4589999999999999986 4799999999999999999999999999999


Q ss_pred             hhCCCCHHHHHHHHHHhHh-cCceeecCCCCCCCCCcc--cHHHHHHHhcc-CCchhHHHHHHhhCCCCCCCC--CCCCC
Q psy8714         307 SGLGMGPHHAMQIAERLYT-QGYVSYPRTETTQYPENF--DLVAVLRQQES-SPDWGDHVREVLSNGISKPRK--GKDVG  380 (562)
Q Consensus       307 ~~~g~s~~~tl~iaQ~LYE-~glISYPRTds~~l~~~~--~~~~~l~~l~~-~~~~~~~~~~~~~~~~~~~~~--~~~~~  380 (562)
                      ++|||||++||++||+||| +||||||||||++||+++  ++.++|..+.. .+.+...+  ++. ...+++.  +++++
T Consensus       303 ~~lg~sa~~Tm~iAQ~LYE~~glITYpRTDS~~ls~~~~~~~~~~i~~~~~~~~~~~~~~--~~~-~~~~~r~~~~~kv~  379 (659)
T 1i7d_A          303 KRFGLSAQNVLDICQKLYETHKLITFPRSDCRYLPEEHFAGRHAVMNAISVHAPDLLPQP--VVD-PDIRNRCWDDKKVD  379 (659)
T ss_dssp             HHHCCCHHHHHHHHHHHHHTSCCBSCSSCCCCCBCGGGGGGHHHHHHHHHHHSTTTCCCT--TCC-TTCCCTTBCGGGCC
T ss_pred             HhcCCCHHHHHHHHHHHHHhCCeEeccCCCCcccCHHHHHHHHHHHHHHhccchhhhhhh--hcc-ccccccccCCCccC
Confidence            9999999999999999999 899999999999999987  67788877642 22222210  000 0123333  34568


Q ss_pred             CCCCCccCCCc-ccCCCCHHHHHHHHHHHHHHHhhcccCceEEEEEEEEEECCeEEEEEEEEEeecceeeeeccccc---
Q psy8714         381 DHPPITPTKLA-TRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAM---  456 (562)
Q Consensus       381 ~H~AI~PT~~~-~~~~L~~~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~v~~~~~~---  456 (562)
                      ||||||||... +.. |+++|++||+||+|||||+||+||+|++|+|.+.++++.|+++|++++++||+.||+.++.   
T Consensus       380 aH~AI~PT~~~~~~~-Ls~de~klY~LI~rRflA~~~~~a~~~~t~v~~~~~~~~F~a~G~~i~~~Gw~~vy~~~~~~~~  458 (659)
T 1i7d_A          380 AHHAIIPTARSSAIN-LTENEAKVYNLIARQYLMQFCPDAVFRKCVIELDIAKGKFVAKARFLAEAGWRTLLGSKERDEE  458 (659)
T ss_dssp             SSCCBCBCSCCSCCC-CCHHHHHHHHHHHHHHHHTTSCCEEEEEEEEEECSTTCCEEECEEEEEECGGGGGSCTTGGGTT
T ss_pred             CCCCcCCcCCCCccC-CCHHHHHHHHHHHHHHHHHhCchheEEEEEEEEEECCEEEEEEEEEEecCChhheecccccccc
Confidence            99999999875 334 9999999999999999999999999999999999999999999999999999999975321   


Q ss_pred             -ccCCCCCCCCCCeeeeeeeEEeeeecCCCCCCCHHHHHHHHHh-----------------cCCCCcCchhHHHHHhhcC
Q psy8714         457 -KNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEK-----------------HGIGTDASIPVHINNICQR  518 (562)
Q Consensus       457 -~~~~Lp~l~~G~~~~~~~~~i~e~~TkPP~~~Te~~Li~~Me~-----------------~GIGTpATra~iI~~L~~r  518 (562)
                       ++..||.+++|+.+.+.++.+.+++|+||+||||++||++||+                 .|||||||||+||++|++|
T Consensus       459 ~~~~~LP~l~~Ge~~~~~~~~~~e~~T~PP~ryTEasLi~~Me~~~k~v~d~e~~~~lk~~~GIGtpATrA~iIe~L~~R  538 (659)
T 1i7d_A          459 NDGTPLPVVAKGDELLCEKGEVVERQTQPPRHFTDATLLSAMTGIARFVQDKDLKKILRATDGLGTEATRAGIIELLFKR  538 (659)
T ss_dssp             CEECCCCCCCTTCEEEEEEEEEEEEECCCCCCEEHHHHHHHHHTGGGGCCCHHHHHHHHHTTSSSCTTTHHHHHHHHHHT
T ss_pred             cccccCCccCCCCEEEEeEeEEeeeecCCCCCCCHHHHHHHHHHhccccCCHHHHHHHhhccCCCccccHHHHHHHHHhC
Confidence             1356999999999999999999999999999999999999994                 6999999999999999999


Q ss_pred             CeEEEcCCCeeecchhHHHHHHhhhccCccCCChhhHHHHHhhC
Q psy8714         519 NYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRVQA  562 (562)
Q Consensus       519 ~Yi~~~~~k~l~~T~~G~~li~~l~~~~~~l~~p~~Ta~~E~~L  562 (562)
                      |||.+ +|+.|+||++|+.|+++|.   ..|++|+|||.||.+|
T Consensus       539 ~Yv~~-~~k~l~pT~~G~~l~~~l~---~~l~~p~~Ta~~E~~L  578 (659)
T 1i7d_A          539 GFLTK-KGRYIHSTDAGKALFHSLP---EMATRPDMTAHWESVL  578 (659)
T ss_dssp             TSEEE-SSSEEEECHHHHHHHHHSC---HHHHSTHHHHHHHHHH
T ss_pred             CcEee-cCCEEeECHHHHHHHHHHH---HHcCCHHHHHHHHHHH
Confidence            99998 6789999999999999864   4599999999999876

>1mw9_X DNA topoisomerase I; decatenase enzyme, toprim domain; HET: DNA; 1.67A {Escherichia coli} SCOP: e.10.1.1 PDB: 1mw8_X* 1cy1_A* 1cy0_A* 1cy2_A* 1cy4_A* 1cy6_A* 1cy7_A* 1cy8_A* 3pwt_A* 3px7_A* 1ecl_A 1cy9_A* 1cyy_A*

Probab=100.00  E-value=1.4e-126  Score=1057.63  Aligned_cols=506  Identities=23%  Similarity=0.348  Sum_probs=428.2

Q ss_pred             eEEEEecccCcCCcchHHhhcccccCCCCceeeeeeeeEcCCCcEEEEEEecccccccccc---------------cCCC
Q psy8714           6 KKLVPASEIKLARPSLISLLTPLQRMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFT---------------SKYN   70 (562)
Q Consensus         6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~~~~~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~~---------------~~y~   70 (562)
                      |+||||||     ||+|+.|++.+|.                  .|+||||+|||++|..+               ++|+
T Consensus         3 k~LiIaEk-----Ps~Ak~Ia~~Lg~------------------~~~Vt~~~GHl~~L~~~~~~~~~~~~~~~~~p~~y~   59 (592)
T 1mw9_X            3 KALVIVES-----PAKAKTINKYLGS------------------DYVVKSSVGHIRDLPTSGSAAKKSADSTSTKTAKKP   59 (592)
T ss_dssp             CEEEEESC-----HHHHHHHHTTSCT------------------TEEEEECCSCCEESCC--------------------
T ss_pred             ceEEEEEC-----HHHHHHHHHHhCC------------------CcEEEeeccccccCCcccccccccccccccchhhhc
Confidence            68999999     9999999977652                  26899999999999653               4554


Q ss_pred             C-----Cc----cCCCCCCCCCCcccccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCC
Q psy8714          71 N-----WD----KVDPLELFSCPTEKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPK  141 (562)
Q Consensus        71 ~-----W~----~~~p~~~~~~~~~~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~  141 (562)
                      .     |.    ..+|.+.|....  .....+.++++.|++++++||.||||||||||||+|||||+++|+.     .++
T Consensus        60 ~~~~~~~~~~~l~i~p~~~f~~~~--~~~~~k~~~~~~lk~l~k~ad~iiiAtD~DREGE~I~~~i~~~~~~-----~~~  132 (592)
T 1mw9_X           60 KKDERGALVNRMGVDPWHNWEAHY--EVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGG-----DDA  132 (592)
T ss_dssp             ---CHHHHHHHHTEETTTTTEECC--EECTTCHHHHHHHHHHHHTCSEEEECCCSSHHHHHHHHHHHHHHCS-----CGG
T ss_pred             hhhhcccchhcCCcCccccCceeE--EEcccHHHHHHHHHHHHhcCCeEEEcCCCCccccHHHHHHHHHhCC-----CCC
Confidence            2     21    123433231110  1112344688899999999999999999999999999999999953     247


Q ss_pred             cEEEEEecccCHHHHHHHHHhCCCChHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhh
Q psy8714         142 TVWRARFSAITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFC  221 (562)
Q Consensus       142 ~v~Rl~~sslt~~~I~~A~~nl~~~~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lI  221 (562)
                      +|+|+|||++|+++|++||+|+++.+.++++||.||+++|||||||+||++|..++        ..+|+||||||||+||
T Consensus       133 ~v~R~~fs~iT~~aI~~A~~~~~~~~~~l~~A~~aR~~~D~lvG~n~Sr~l~~~~~--------~~lS~GRVQtptL~lI  204 (592)
T 1mw9_X          133 RYSRVVFNEITKNAIRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVSPLLWKKIA--------RGLSAGRVQSVAVRLV  204 (592)
T ss_dssp             GEEECCCSSCSHHHHHHHHHSCBCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC--------TTCCCCTTHHHHHHHH
T ss_pred             CeEEEEEccCCHHHHHHHHhCCccccHHHHHHHHHHHHHHHHhhHhhhHHHHhhhc--------cccccCccchhHHHHH
Confidence            89999999999999999999999999999999999999999999999999987542        2599999999999999


Q ss_pred             hhhhhhhhcccCcceEEEEEEEee-CCeEEEEEeec-----ccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCC
Q psy8714         222 VERHDKIRTFKPEPYWLLDLTLNL-NGVAVSVTWSR-----GHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQA  295 (562)
Q Consensus       222 v~Re~eI~~F~p~~y~~i~~~~~~-~~~~~~~~~~~-----~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~p  295 (562)
                      |+||+||++|+|++||.|.+.+.. ++..|.+.|..     .++.+++.|+.+++.|.+ +.++|.+|++++++++||+|
T Consensus       205 v~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~l~~-~~~~V~~v~~k~~~~~pP~p  283 (592)
T 1mw9_X          205 VEREREIKAFVPEEFWEVDASTTTPSGEALALQVTHQNDKPFRPVNKEQTQAAVSLLEK-ARYSVLEREDKPTTSKPGAP  283 (592)
T ss_dssp             HHHHHHHHHCCCCEEEEEEEEEECTTCCEEEEEEEEETTEECCCCSHHHHHHHHHHHHH-CCEEEEEEEEEEEEECCCCC
T ss_pred             HHHHHHHHhCCCcceEEEEEEEecCCCcEEEEEEEecCCcccccCCHHHHHHHHHHhcC-CCeEEEEEEEEEEeccCCCC
Confidence            999999999999999999999965 45568887742     367899999999999976 47999999999999999999


Q ss_pred             CCHHHHHHHHHhhCCCCHHHHHHHHHHhHhcCceeecCCCCCCCCCcc--cHHHHHHHhccCCchhHHHHHHhhCCCCCC
Q psy8714         296 LNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENF--DLVAVLRQQESSPDWGDHVREVLSNGISKP  373 (562)
Q Consensus       296 f~l~~Lq~~a~~~~g~s~~~tl~iaQ~LYE~glISYPRTds~~l~~~~--~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~  373 (562)
                      |+|++||++||++|||||++||++||+|||+||||||||||++||+++  .+...+..+.     +.   .++..   .+
T Consensus       284 f~ts~LQ~~As~~lg~sa~~tm~iAQ~LYE~glITYpRTDs~~ls~~~~~~~~~~i~~~~-----g~---~~~~~---~~  352 (592)
T 1mw9_X          284 FITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYITYMRTDSTNLSQDAVNMVRGYISDNF-----GK---KYLPE---SP  352 (592)
T ss_dssp             BCHHHHHHHHHHHHCCCHHHHHHHHHHHHHTTSBCCSCCCCCCCCHHHHHHHHHHHHHHT-----CG---GGSCS---SC
T ss_pred             ccHHHHHHHHHHhhCCCHHHHHHHHHHHHhCCeeeccCCCCCccCHHHHHHHHHHHHHhh-----hh---hhccc---CC
Confidence            999999999999999999999999999999999999999999999975  3455554431     11   11221   22


Q ss_pred             CCC----CCCCCCCCCccCCCc----ccCCCCHHHHHHHHHHHHHHHhhcccCceEEEEEEEEEECCeEEEEEEEEEeec
Q psy8714         374 RKG----KDVGDHPPITPTKLA----TRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHP  445 (562)
Q Consensus       374 ~~~----~~~~~H~AI~PT~~~----~~~~L~~~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~  445 (562)
                      +..    ++.+||||||||...    ....|+++|++||+||+||||||||+||+|++|+|.+.++++.|+++|++++++
T Consensus       353 ~~~~~~~~~~~aH~AI~PT~~~~~~~~l~~Ls~~e~klY~LI~rrflA~~~~~a~~~~t~v~~~~~~~~F~a~g~~i~~~  432 (592)
T 1mw9_X          353 NQYASKENSQEAREAIRPSDVNVMAESLKDMEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFD  432 (592)
T ss_dssp             CCCC--------CCCBCBSCTTCCGGGCSSCCHHHHHHHHHHHHHHHHHTSCCEEEEEEEEEEEETTEEEEEEEEEEEEC
T ss_pred             ccccCCCCCCCCCCCEecccCccCccchhhCCHHHHHHHHHHHHHHHHHhCchhEEEEEEEEEEECCEEEEEEEEEEeeC
Confidence            211    123789999999742    225799999999999999999999999999999999999999999999999999


Q ss_pred             ceeeeeccccc--ccCCCCCCCCCCeeeeeeeEEeeeecCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEE
Q psy8714         446 GFTGVMTWSAM--KNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTV  523 (562)
Q Consensus       446 Gw~~v~~~~~~--~~~~Lp~l~~G~~~~~~~~~i~e~~TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~  523 (562)
                      ||+.||+....  ++..||.+++|+.+.+.++.+.+++|+||+||||++||++||+.|||||||||+||++|++||||.+
T Consensus       433 Gw~~vy~~~~~~~~~~~LP~l~~G~~~~~~~~~~~~~~T~PP~ryTEasLi~~Me~~GIGtpATrA~iI~~L~~R~Yv~~  512 (592)
T 1mw9_X          433 GWTKVMPALRKGDEDRILPAVNKGDALTLVELTPAQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRV  512 (592)
T ss_dssp             GGGGGSCCC----CCCCCCCCCTTCEEEEEEEEEEEEECCCCCCCCHHHHHHHHHHTTCCCTTTHHHHHHHHHHTTSEEE
T ss_pred             ChHHhcCccccccccccccccCCCCEeEeeEeEEeeeeccCCCCCCHHHHHHHHHhcCCCchhhHHHHHHHHHhcCceee
Confidence            99999975432  2557999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cCCCeeecchhHHHHHHhhhccCccCCChhhHHHHHhhC
Q psy8714         524 TSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRVQA  562 (562)
Q Consensus       524 ~~~k~l~~T~~G~~li~~l~~~~~~l~~p~~Ta~~E~~L  562 (562)
                       +|++|+||++|+.|++.|...++.|++|+|||.||.+|
T Consensus       513 -~~k~l~pT~~G~~l~~~L~~~~~~l~~~~~Ta~~E~~L  550 (592)
T 1mw9_X          513 -ENRRFYAEKMGEIVTDRLEENFRELMNYDFTAQMENNL  550 (592)
T ss_dssp             -ETTEEEECHHHHHHHHHHHHHCHHHHCHHHHHHHHHHH
T ss_pred             -cCCEeeecHHHHHHHHHHHHhhhhhCCHHHHHHHHHHH
Confidence             57899999999999999877777899999999999875

>2gai_A DNA topoisomerase I; zinc ribbon; HET: DNA; 1.70A {Thermotoga maritima} PDB: 2gaj_A*

Probab=100.00  E-value=5.7e-125  Score=1050.77  Aligned_cols=495  Identities=24%  Similarity=0.341  Sum_probs=422.4

Q ss_pred             CcccceEEEEecccCcCCcchHHhhcccccCCCCceeeeeeeeEcCCCcEEEEEEecccccccccccCCCCCccCCCCCC
Q psy8714           1 MHLRVKKLVPASEIKLARPSLISLLTPLQRMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLEL   80 (562)
Q Consensus         1 ~~~~~~~l~~ae~~~~~~p~~a~~~~~~~g~~~~~~~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~~~~y~~W~~~~p~~~   80 (562)
                      |.-+.|.||||||     ||+|+.|++.+|.                +  |+|+||+|||++|..|.  -.|...+|   
T Consensus         1 ~~~~mk~LvIaEk-----Ps~Ak~Ia~~Lg~----------------~--y~Vt~s~GHl~~l~~~~--~~~~~~~~---   52 (633)
T 2gai_A            1 MAKKVKKYIVVES-----PAKAKTIKSILGN----------------E--YEVFASMGHIIDLPKSK--FGVDLEKD---   52 (633)
T ss_dssp             ------CEEEESC-----HHHHHHHHHHHGG----------------G--SEEEECCSCSEESCSSS--CCEETTTT---
T ss_pred             CCCCCcEEEEEeC-----HHHHHHHHHHhCC----------------C--CEEEecccccccCCccC--CCCCcccC---
Confidence            4445578999999     9999999987752                1  57999999999996542  24554332   


Q ss_pred             CCCCcccccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHHHH
Q psy8714          81 FSCPTEKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAM  160 (562)
Q Consensus        81 ~~~~~~~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~A~  160 (562)
                      |. |.. .....+.++++.|++++++|| ||||||||||||+|||||+++++      ++++|+|+|||++|+++|++||
T Consensus        53 f~-p~~-~~~~~~~~~~~~lk~l~k~ad-iiiAtD~DREGE~I~~~i~~~~~------~~~~v~R~~fs~iT~~aI~~a~  123 (633)
T 2gai_A           53 FE-PEF-AVIKGKEKVVEKLKDLAKKGE-LLIASDMDREGEAIAWHIARVTN------TLGRKNRIVFSEITPRVIREAV  123 (633)
T ss_dssp             SE-ECC-EECTTCHHHHHHHHHHHHHSC-EEECCCSSHHHHHHHHHHHHHHT------CTTSSCBCCCSSCCHHHHHHHH
T ss_pred             cC-ceE-EECccHHHHHHHHHHHHhhCC-EEEcCCCCcccCHHHHHHHHHcC------CCCCeEEEEEccCCHHHHHHHH
Confidence            21 111 111234568888999999999 99999999999999999999995      3589999999999999999999


Q ss_pred             HhCCCChHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhhhhhhhhhhcccCcceEEEE
Q psy8714         161 WNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLD  240 (562)
Q Consensus       161 ~nl~~~~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lIv~Re~eI~~F~p~~y~~i~  240 (562)
                      +||++++.++++||.||+++|||||||+||++|+.++        ..+|+||||||||+|||+||+||++|+|++||+|.
T Consensus       124 ~~~~~~~~~l~~A~~aR~~~D~lvG~n~Sr~l~~~~~--------~~lS~GRVQtptL~lIv~Re~eI~~F~p~~y~~i~  195 (633)
T 2gai_A          124 KNPREIDMKKVRAQLARRILDRIVGYSLSPVLWRNFK--------SNLSAGRVQSATLKLVCDREREILRFVPKKYHRIT  195 (633)
T ss_dssp             HSCBCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS--------CCCTTHHHHHHHHHHHHHHHHHHHHCCCCEEEEEE
T ss_pred             hCCCCCcHHHHHHHHHhhHHHHHhhHHHCHHHHHhhh--------cccccCccchHHHHHHHHHHHHHHhCCCcceEEEE
Confidence            9999999999999999999999999999999998653        25999999999999999999999999999999999


Q ss_pred             EEEeeCCeEEEEEe--ecccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHHHHHHHHHhhCCCCHHHHHH
Q psy8714         241 LTLNLNGVAVSVTW--SRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQ  318 (562)
Q Consensus       241 ~~~~~~~~~~~~~~--~~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl~  318 (562)
                      +.+.  +  |.+.|  ...+++|++.|++++ .|   +.++|.+|+.++++++||+||+|++||++||++|||||++||+
T Consensus       196 ~~~~--~--~~a~~~~~~~~~~~~~~a~~~~-~~---~~~~V~~v~~k~~~~~pP~pf~ts~LQ~~As~~lg~sa~~tm~  267 (633)
T 2gai_A          196 VNFD--G--LTAEIDVKEKKFFDAETLKEIQ-SI---DELVVEEKKVSVKKFAPPEPFKTSTLQQEAYSKLGFSVSKTMM  267 (633)
T ss_dssp             EEET--T--EEEEECCSSCCCCCHHHHHHHH-TC---CCEEEEEEEEEEEEECCCCCBCHHHHHHHHHHHHCCCHHHHHH
T ss_pred             EEEe--e--EEEEEecCCcccCCHHHHHHHH-hC---CCeEEEEEEEEEEEecCCCCccHHHHHHHHHHHcCCCHHHHHH
Confidence            9984  2  88887  445788999999999 77   4689999999999999999999999999999999999999999


Q ss_pred             HHHHhHhc--------CceeecCCCCCCCCCcc--cHHHHHHHhccCCchhHHHHHHhhCCCCCCC---CCCCC-CCCCC
Q psy8714         319 IAERLYTQ--------GYVSYPRTETTQYPENF--DLVAVLRQQESSPDWGDHVREVLSNGISKPR---KGKDV-GDHPP  384 (562)
Q Consensus       319 iaQ~LYE~--------glISYPRTds~~l~~~~--~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~---~~~~~-~~H~A  384 (562)
                      +||+|||+        ||||||||||++||+++  .+.+.|....     +.   .++..   .|+   +.+++ +||||
T Consensus       268 iaQ~LYE~~~~~~~~~glITYpRTDs~~ls~~~~~~~~~~i~~~~-----g~---~~~~~---~~r~~~~~~~~~~aH~A  336 (633)
T 2gai_A          268 IAQQLYEGVETKDGHIAFITYMRTDSTRVSDYAKEEARNLITEVF-----GE---EYVGS---KRERRKSNAKIQDAHEA  336 (633)
T ss_dssp             HHHHHHHCEECSSSEECCBCCSCCSCCCCCHHHHHHHHHHHHHHT-----CG---GGBC-----------------CCCC
T ss_pred             HHHHHhhccccccCccceEEecCCCccccCHHHHHHHHHHHHHHh-----hh---hhccc---CCccccCCCCcCCCCCC
Confidence            99999998        99999999999999976  2455554321     11   11211   122   12344 47999


Q ss_pred             CccCCCc-c----cCCCCHHHHHHHHHHHHHHHhhcccCceEEEEEEEEEE--CCeEEEEEEEEEeecceeeeecccccc
Q psy8714         385 ITPTKLA-T----RTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSV--ADEMFTMEAKYLLHPGFTGVMTWSAMK  457 (562)
Q Consensus       385 I~PT~~~-~----~~~L~~~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~--~~~~F~a~g~~~~~~Gw~~v~~~~~~~  457 (562)
                      ||||... .    ...|+++|++||+||+|||||+||+||+|++|+|.+.+  +++.|+++|++++++||+.||..  ++
T Consensus       337 I~PT~~~~~p~~~~~~L~~~e~klY~LI~rrflA~~~~~a~~~~t~v~~~~~~~~~~F~a~g~~i~~~G~~~vy~~--~~  414 (633)
T 2gai_A          337 IRPTNVFMTPEEAGKYLNSDQKKLYELIWKRFLASQMKPSQYEETRFVLRTKDGKYRFKGTVLKKIFDGYEKVWKT--ER  414 (633)
T ss_dssp             BCBSCTTSCHHHHTTTSCHHHHHHHHHHHHHHHHHTBCCEEEEEEEEEEECTTSSCEEEEEEEEEEECGGGGTSCC--CC
T ss_pred             cccccccCChhhhhhcCCHHHHHHHHHHHHHHHHHhCchheEEEEEEEEEEeCCCcEEEEEEEEEecCCHHHhhcc--cc
Confidence            9999863 2    14699999999999999999999999999999999999  99999999999999999999942  23


Q ss_pred             cCCCCCCCCCCeeeeeeeEEeeeecCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEcCCCeeecchhHHH
Q psy8714         458 NESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIV  537 (562)
Q Consensus       458 ~~~Lp~l~~G~~~~~~~~~i~e~~TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~~~k~l~~T~~G~~  537 (562)
                      +..||.+++|+.+.+.++.+.+++|+||+||||++||++||+.|||||||||+||++|++||||.+ +|+.|+||++|+.
T Consensus       415 ~~~LP~l~~G~~~~~~~~~~~~~~T~PP~ryTEasLi~~Me~~GIGtpaT~A~iI~~L~~R~Yv~~-~~k~l~pT~~G~~  493 (633)
T 2gai_A          415 NTGEFPFEEGESVKPVVVKIEEQETKPKPRYTEGSLVKEMERLGIGRPSTYASTIKLLLNRGYIKK-IRGYLYPTIVGSV  493 (633)
T ss_dssp             CBCCCCCCTTCEECCCEEEEEEEECCCCCCCCHHHHHHHHHHHTCCCTTTHHHHHHHHHHTTSEEE-ETTEEEEBHHHHH
T ss_pred             cccCCCcCCCCEEEEeEEEEeeeecCCCCCCCHHHHHHHhhccCCCCcccHHHHHHHHhhcCcEEE-cCCEEEEChhHHH
Confidence            557999999999999999999999999999999999999999999999999999999999999998 5789999999999


Q ss_pred             HHHhhhccCccCCChhhHHHHHhhC
Q psy8714         538 LVHGYQKIDRELVEPTMRSAYRVQA  562 (562)
Q Consensus       538 li~~l~~~~~~l~~p~~Ta~~E~~L  562 (562)
                      |+++|...++.|++|+|||.||.+|
T Consensus       494 l~~~l~~~~~~l~~~~~Ta~~E~~L  518 (633)
T 2gai_A          494 VMDYLEKKYSDVVSVSFTAEMEKDL  518 (633)
T ss_dssp             HHHHHHHHSTTTTSHHHHHHHHHHH
T ss_pred             HHHHHHHhhhhhcCHHHHHHHHHHH
Confidence            9999988788999999999999875

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=100.00  E-value=1.8e-113  Score=1015.65  Aligned_cols=494  Identities=21%  Similarity=0.296  Sum_probs=414.8

Q ss_pred             eEEEEecccCcCCcchHHhhcccccCCCC-----ceeeeeeeeEcCCCcEEEEEEecccccccccccCCCCCccCC-C-C
Q psy8714           6 KKLVPASEIKLARPSLISLLTPLQRMNGA-----CSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVD-P-L   78 (562)
Q Consensus         6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~~-----~~~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~~~~y~~W~~~~-p-~   78 (562)
                      +.||||||     ||+|+.|++++|....     +++|+|   ..|+++ |+|||+.|||++|..|++|..|...+ + .
T Consensus       542 ~~LvIaEk-----Ps~Ak~ia~~Lg~~~~~~~~~~~~ye~---~~~~~~-~~v~~~~GHl~~l~~~~~~~~~~~~~~~~~  612 (1104)
T 4ddu_A          542 SLLIIVES-----PTKAETLSRFLGRASSRKERNIIVHEA---VTGEGV-ILFTATRGHVYDLVTKGGIHGVEEENGKFV  612 (1104)
T ss_dssp             CEEEEESC-----HHHHHHHHHHHTCCEEEEETTEEEEEE---EETTEE-EEEEECCSCCEEECSSSTBTTBEEETTEEE
T ss_pred             CeEEEEEC-----HHHHHHHHHHhCCCccccCCCceeEEE---ecCCce-EEEEEeccccccCCCccccCccccccCCcC
Confidence            57999999     9999999999997632     223333   235543 69999999999999888876554322 1 0


Q ss_pred             CCCC----C--------------Cc-ccccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCC
Q psy8714          79 ELFS----C--------------PT-EKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININS  139 (562)
Q Consensus        79 ~~~~----~--------------~~-~~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~  139 (562)
                      +.|.    +              |. .......+.++++.|++++++||+||||||||||||+|||||+++++.     +
T Consensus       613 p~y~~~~~~~~~~~~f~~~~~~~p~~~~~~~~~~~~~~~~lk~~~~~~d~i~~atD~DrEGE~I~~~i~~~~~~-----~  687 (1104)
T 4ddu_A          613 PVYNSLKRCRDCGYQFTEDRDECPVCSSKNIDDKTETLRALREISLEADEILVATDPDVEGEKISWDVTQYLLP-----S  687 (1104)
T ss_dssp             CEEEECEEETTTCCEECSCCSSCTTTCCSCEEEHHHHHHHHHHHTTTCSEEEECCCSSHHHHHHHHHHHHHHTT-----T
T ss_pred             ccccccccccchhhhhccccccccccccccCccHHHHHHHHHHHHhcCCEEEECcCCchhHHHHHHHHHHHhcc-----c
Confidence            1111    0              10 000011345688999999999999999999999999999999999963     3


Q ss_pred             CCcEEEEEecccCHHHHHHHHHhCCCChHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchh
Q psy8714         140 PKTVWRARFSAITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLG  219 (562)
Q Consensus       140 ~~~v~Rl~~sslt~~~I~~A~~nl~~~~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~  219 (562)
                      +++|+|+|||++|+++|++||+||+++++++++||.||+++|||||||+||++|..++       ++.+|+||||||||+
T Consensus       688 ~~~~~R~~f~~it~~aI~~a~~~~~~~~~~l~~a~~aR~~~D~lvG~~~sr~l~~~~~-------~~~lS~GRVQtptL~  760 (1104)
T 4ddu_A          688 TRSLRRIEMHEITRYGFKKARESVRFVDFNLVKAQIVRRVQDRWIGFELSGKLQKRFG-------RSNLSAGRVQSTVLG  760 (1104)
T ss_dssp             CSCEEECCCSSSSHHHHHHHHHTCBCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-------CSCCCCCHHHHHHHH
T ss_pred             CCCeEEEEEccCCHHHHHHHHhCCCcCchhHHHHHHHHHHHHHHHHHHHhHHHHHhhC-------CcccccCccccHHHH
Confidence            6899999999999999999999999999999999999999999999999999987653       236999999999999


Q ss_pred             hhhhhhhhhhcccCcceEEEEEEEeeCCeEEEEEeecccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHH
Q psy8714         220 FCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTV  299 (562)
Q Consensus       220 lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~  299 (562)
                      |||+||+||+  +|++||+|.  ...++..|.+.|.+.                 .+.++|+++++++++++||+||||+
T Consensus       761 liv~Re~ei~--~~~~~~~i~--~~~~~~~~~~~~~~~-----------------~~~~~V~~v~~k~~~~~pp~pf~t~  819 (1104)
T 4ddu_A          761 WIVEREEEYK--KSEKDFTLL--VLENGVNLEVEGKIA-----------------DDVVTVVELQEAEEEKNPLPPYTTS  819 (1104)
T ss_dssp             HHHHHHHTTT--TCCCCEEEE--EETTSCEEEEESCCC-----------------CCEEEEEEEEEEEEEECCCCCBCHH
T ss_pred             HHHHHHHHHh--ccCcEEEEE--EecCcEEEEeecccc-----------------CCcEEEEEEEeeeEEecCCCCCCHH
Confidence            9999999999  678999993  334566666666542                 2478999999999999999999999


Q ss_pred             HHHHHHHhhCCCCHHHHHHHHHHhHhcCceeecCCCCCCCCCcc--cHHHHHHHhccCCchhHHHHHHhhCCCCCCCCCC
Q psy8714         300 ELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENF--DLVAVLRQQESSPDWGDHVREVLSNGISKPRKGK  377 (562)
Q Consensus       300 ~Lq~~a~~~~g~s~~~tl~iaQ~LYE~glISYPRTds~~l~~~~--~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~  377 (562)
                      +||++||++|||||++||++||+|||+||||||||||++||++.  .+.+.+..+.             .....+||.++
T Consensus       820 ~Lq~~a~~~~g~s~~~tm~iaQ~LYe~g~iTYpRTds~~l~~~~~~~~~~~i~~~~-------------~~~~~~~r~~~  886 (1104)
T 4ddu_A          820 SALSEISQKLRLGVQEVMDILQDLFEKGFITYHRTDSTRISLEGQNVARTYLRKIG-------------KEDIFMGRSWS  886 (1104)
T ss_dssp             HHHHHHHHHSSCCHHHHHHHHHHHHHTTSBSCSCCSCCCCCHHHHHHHHHHHHHHS-------------CGGGBCCCCCC
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHhCCceeecCCCccccCHHHHHHHHHHHHHhh-------------CccccCCCCCC
Confidence            99999999999999999999999999999999999999999864  2334444332             11123566777


Q ss_pred             CCCCCCCCccCCCcc------------cCCCCHHHHHHHHHHHHHHHhhcccCceEEEEEEEEEECCeEEEEEEE-EEee
Q psy8714         378 DVGDHPPITPTKLAT------------RTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAK-YLLH  444 (562)
Q Consensus       378 ~~~~H~AI~PT~~~~------------~~~L~~~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~~~F~a~g~-~~~~  444 (562)
                      +.+||||||||...+            ...|+++|++||+||||||||+||+||+|++|++.+.++++.|+++|+ ++++
T Consensus       887 ~~~aH~aI~Pt~~~~~~~~~~~~~~~~~~~l~~~e~~lY~lI~~rfla~~~~~a~~~~t~v~~~~~~~~f~~~g~~~i~~  966 (1104)
T 4ddu_A          887 TEGAHEAIRPVKPIDARELEEMIEEGLIADLTKKHLRVYELIFNRFLASQSAAVKVKKQIVTVDVDGKRMGIEQIVEILR  966 (1104)
T ss_dssp             SSCSSCCBCBSSSCCHHHHHHHHHHTSSCCCCHHHHHHHHHHHHHHHHHHBCCEEEEEEEEEEESSSCEEEEEEEEEEEE
T ss_pred             CCCCCcCcCCCccCChHhhhhhhcccccccCCHHHHHHHHHHHHHHHHHhCCceeEEEEEEEEEECCEEEEEEEEEEEEE
Confidence            779999999997632            136999999999999999999999999999999999999999999997 7899


Q ss_pred             cceeeeecccccccCCCCCCCCCCeeeeeeeEEeeeecCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEc
Q psy8714         445 PGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVT  524 (562)
Q Consensus       445 ~Gw~~v~~~~~~~~~~Lp~l~~G~~~~~~~~~i~e~~TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~  524 (562)
                      +||+.+|+.     ..||.+++| .+.+.++  ..++|+||+||||++||++||+.|||||||||+||++|++||||.++
T Consensus       967 ~G~~~v~~~-----~~lp~l~~g-~~~~~~~--~~~~~~~p~~~tea~Li~~me~~GIGtpaT~a~iI~~l~~r~Yv~~~ 1038 (1104)
T 4ddu_A          967 DGWNLFVPL-----TVSPRFEHR-TYKIKEK--KFYKKHTVPLFTQASIVEEMKKRGIGRPSTYAKIVEVLFRRGYVYED 1038 (1104)
T ss_dssp             CSGGGTSCC-----CCCCCCCSS-EEEEEEE--EEECCCSSCCBCHHHHHHHHHHHTCSCTTTHHHHHHHHHHTTSEEEC
T ss_pred             CCHHHhccc-----ccCCCCCCC-ceEEEEe--eeeecCCCCCCCHHHHHHHHHhcCCCCccchHHHHHHHHhCCeEEEc
Confidence            999999962     469999999 6766554  44888889999999999999999999999999999999999999984


Q ss_pred             CCCeeecchhHHHHHHhhhccCccCCChhhHHHHHhhC
Q psy8714         525 SGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRVQA  562 (562)
Q Consensus       525 ~~k~l~~T~~G~~li~~l~~~~~~l~~p~~Ta~~E~~L  562 (562)
                      +++.|+||++|+.|++.|...++.|++|+|||.||.+|
T Consensus      1039 ~~~~l~pT~~G~~l~~~l~~~~~~l~~~~~Ta~~E~~l 1076 (1104)
T 4ddu_A         1039 KYKRVRPTRFGVMVYSYLKERYEKYVTEETTRRLEEIM 1076 (1104)
T ss_dssp             TTCCEEECHHHHHHHHHHHHHCGGGTCHHHHHHHHHHH
T ss_pred             CCCeEeEchHHHHHHHHHHHhchhhcCHHHHHHHHHHH
Confidence            33899999999999999977778999999999999875

>1gku_B Reverse gyrase, TOP-RG; topoisomerase, DNA supercoiling, archaea, helicase; 2.7A {Archaeoglobus fulgidus} SCOP: c.37.1.16 c.37.1.16 e.10.1.1 PDB: 1gl9_B*

Probab=100.00  E-value=1.8e-111  Score=997.67  Aligned_cols=482  Identities=20%  Similarity=0.271  Sum_probs=401.4

Q ss_pred             eEEEEecccCcCCcchHHhhcccccCC-----CCceeeeeeeeEcCCCcEEEEEEecccccccccccCC-CCCccCCC-C
Q psy8714           6 KKLVPASEIKLARPSLISLLTPLQRMN-----GACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKY-NNWDKVDP-L   78 (562)
Q Consensus         6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~-----~~~~~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~~~~y-~~W~~~~p-~   78 (562)
                      |.||||||     ||+|+.|++++|..     +++++|+|   ..|+ ..|+||||.|||++|+.|++| +.|. .++ .
T Consensus       506 ~~LiIaEk-----Ps~ak~ia~~Lg~~~~~~~~~~~~ye~---~~~~-~~~~vt~~~GHl~~l~~~~~~~~~~~-~~~~~  575 (1054)
T 1gku_B          506 PALFIVES-----PTKARQISRFFGKPSVKVLDGAVVYEI---PMQK-YVLMVTASIGHVVDLITNRGFHGVLV-NGRFV  575 (1054)
T ss_dssp             EEEEEESC-----HHHHHHHHGGGEECEEEEETTEEEEEE---ECSS-EEEEEEECCSCSEEECSSSSTTSSCC-SSSCC
T ss_pred             CEEEEEEC-----HHHHHHHHHHhCCCcccCCCCceeEEe---ecCC-ceEEEEEeccccccCCCchhhcCccc-ccCcC
Confidence            46999999     99999999999864     22222322   1344 346899999999999988864 4565 331 1


Q ss_pred             CCCCCCc------------------c-cccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCC
Q psy8714          79 ELFSCPT------------------E-KREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININS  139 (562)
Q Consensus        79 ~~~~~~~------------------~-~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~  139 (562)
                      +.++...                  . .....++.++++.|++++++||.||||||||||||+|||||+++++      +
T Consensus       576 P~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~l~~l~~~~d~ii~atD~DrEGE~I~~~i~~~~~------~  649 (1054)
T 1gku_B          576 PVYASIKRCRDCGYQFTEDRESCPKCGSENVDNSRSRIEALRKLAHDAEFVIVGTDPDTEGEKIAWDLKNLLS------G  649 (1054)
T ss_dssp             CEEEECC------------------------CCHHHHHHHHHHHHHHHSEEEECCCSSHHHHHHHHHHHHHHT------T
T ss_pred             CcccccccccchhhhcccccccccccccccCccHHHHHHHHHHHHhcCCEEEECCCCChhhhHHHHHHHHHhC------C
Confidence            2222110                  0 0011234578889999999999999999999999999999999993      4


Q ss_pred             CCcEEEEEecccCHHHHHHHHHhCCCChHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchh
Q psy8714         140 PKTVWRARFSAITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLG  219 (562)
Q Consensus       140 ~~~v~Rl~~sslt~~~I~~A~~nl~~~~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~  219 (562)
                      +++|+|+|||++|+++|++||+||++++.++++||.||+++|||||||+||++|..+.       ++.+|+||||||||+
T Consensus       650 ~~~~~R~~~~~it~~aI~~a~~~~~~~~~~l~~a~~aR~~~D~lvG~~~sr~l~~~~~-------~~~lS~GRVQtptL~  722 (1054)
T 1gku_B          650 CGAVKRAEFHEVTRRAILEALESLRDVDENLVKAQVVRRIEDRWIGFVLSQKLWERFN-------NRNLSAGRAQTLVLG  722 (1054)
T ss_dssp             SSEEEECCCSBCSHHHHHHHHTSCBCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTT-------CSSCCCCTTHHHHHH
T ss_pred             CCCeEEEEEccCCHHHHHHHHhCCCCCcHhHHHHHHhHHHHHHHHHHHhCHHHHHhcc-------CceeeeccccchHHH
Confidence            6899999999999999999999999999999999999999999999999999986542       246999999999999


Q ss_pred             hhhhhhhhhhcccCcceEEEEEEEeeCCeEEEEEeecccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHH
Q psy8714         220 FCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTV  299 (562)
Q Consensus       220 lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~  299 (562)
                      |||+||+||   +|++||.+.     +|..|.+.|.+.             .+    .++|++|++++++++||+||||+
T Consensus       723 ~iv~Re~ei---~~~~~~~~~-----~~~~~~~~~~~~-------------~~----~~~V~~v~~k~~~~~pp~pf~~~  777 (1054)
T 1gku_B          723 WIIDRFQES---RERRKIAIV-----RDFDLVLEHDEE-------------EF----DLTIKLVEEREELRTPLPPYTTE  777 (1054)
T ss_dssp             HHHHHHTGG---GSEEEEEEE-----TTTTEEESCCCS-------------EE----EEEEEEEEEEEEEECCCCCBCHH
T ss_pred             HHHHHHHhh---CCcCcEEEE-----CCEEEEeccccc-------------ce----EEEEEEEEeeEEEecCCCCCCHH
Confidence            999999999   688999874     455566544321             11    57999999999999999999999


Q ss_pred             HHHHHHHhhCCCCHHHHHHHHHHhHhcCceeecCCCCCCCCCcccHHHHHHHhccCCchhHHHHHHhhCCCCCCCCCCCC
Q psy8714         300 ELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDV  379 (562)
Q Consensus       300 ~Lq~~a~~~~g~s~~~tl~iaQ~LYE~glISYPRTds~~l~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~  379 (562)
                      +||++||++|||||++||++||+|||+||||||||||++||++.  .+.+.             .++..+. +||.+++.
T Consensus       778 ~Lq~~a~~~~g~s~~~tm~iaQ~LYe~g~iTYpRTds~~l~~~~--~~~~~-------------~~~~~~~-~~r~~~~~  841 (1054)
T 1gku_B          778 TMLSDANRILKFSVKQTMQIAQELFENGLITYHRTDSTRVSDVG--QRIAK-------------EYLGDDF-VGREWGES  841 (1054)
T ss_dssp             HHHHHHHHTSCCCHHHHHHHHHHHHHTTSBBCSSCCCCCCCHHH--HHHHH-------------HHHTTSB-CCCCSCSC
T ss_pred             HHHHHHHHHhCCCHHHHHHHHHHHHhcCceeecCCCccccCHHH--HHHHH-------------HHhhhhh-ccccCCCC
Confidence            99999999999999999999999999999999999999999864  11111             2222223 56766666


Q ss_pred             CCCCCCccCCCccc--------------CCCCHHHHHHHHHHHHHHHhhcccCceEEEEEEEEEECCeEEEEE-EEEEee
Q psy8714         380 GDHPPITPTKLATR--------------TQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTME-AKYLLH  444 (562)
Q Consensus       380 ~~H~AI~PT~~~~~--------------~~L~~~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~~~F~a~-g~~~~~  444 (562)
                      +||||||||...+.              ..|+++|++||+||+|||||+||+||+|++|++.+.++++.|+++ |.++++
T Consensus       842 ~aH~aI~Pt~~~~~~~~~~~~~~~~~~~~~l~~~e~~lY~lI~~rfla~~~~~a~~~~t~v~~~~~~~~f~~~~~~~~~~  921 (1054)
T 1gku_B          842 GAHECIRPTRPLTRDDVQRLIQEGVLVVEGLRWEHFALYDLIFRRFMASQCRPFKVVVKKYSIEFDGKTAEEERIVRAEG  921 (1054)
T ss_dssp             CSCCCBCBSSSCCHHHHHHHHHHTCSCCSSCCHHHHHHHHHHHHHHHHTTBCCEEEEEEEEEEEETTEEEEECCEEEEES
T ss_pred             CCCCCCCCCCCCChHHHhhhhhcccccccCCCHHHHHHHHHHHHHHHHHhCcceEEEEEEEEEEeCCEEEEEEeeEEEEe
Confidence            89999999986321              269999999999999999999999999999999999999999999 578999


Q ss_pred             cceeeeecccccccCCCCCCCCCCeeeeeeeEEeeeecCCC-CCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEE
Q psy8714         445 PGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKMVERKTTPP-DYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTV  523 (562)
Q Consensus       445 ~Gw~~v~~~~~~~~~~Lp~l~~G~~~~~~~~~i~e~~TkPP-~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~  523 (562)
                      +||+.+|+++     .+|.+++|+ +.+.    .+++|+|| +||||++||++||+.|||||||||+||++|++||||..
T Consensus       922 ~G~~~v~~~~-----~~~~l~~g~-~~~~----~~~~t~pp~~~~tea~Li~~Me~~GIGtpaT~a~iI~~l~~r~Yv~~  991 (1054)
T 1gku_B          922 RAYELYRAVW-----VKNELPTGT-FRVK----AEVKSVPKVLPFTQSEIIQMMKERGIGRPSTYATIVDRLFMRNYVVE  991 (1054)
T ss_dssp             HHHHHSCCSC-----CCCCCCCEE-EEEE----BCCEEEESSCCBCHHHHHHHHHHHTCCCTTTHHHHHHHHHHTTSEEE
T ss_pred             CCceEEeccc-----cCCCCCCCc-eEEe----eeeeeCCCCCCCCHHHHHHhhhcCCCCCcccHHHHHHHHHhCCchhh
Confidence            9999999643     378899995 5443    68999998 79999999999999999999999999999999999987


Q ss_pred             cCCCeeecchhHHHHHHhhhccCccCCChhhHHHHHhhC
Q psy8714         524 TSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRVQA  562 (562)
Q Consensus       524 ~~~k~l~~T~~G~~li~~l~~~~~~l~~p~~Ta~~E~~L  562 (562)
                      ++ ++|+||++|+.|+++|...++.|++|+|||.||.+|
T Consensus       992 ~~-~~l~pT~~G~~l~~~l~~~~~~l~~~~~Ta~~E~~l 1029 (1054)
T 1gku_B          992 KY-GRMIPTKLGIDVFRFLVRRYAKFVSEDRTRDLESRM 1029 (1054)
T ss_dssp             ET-TEEEECHHHHHHHHHHHHSCCGGGSHHHHHHHHHHH
T ss_pred             cC-CEEeEchHHHHHHHHHHHhhhhhCCHHHHHHHHHHH
Confidence            44 469999999999999987778899999999999875

>1vdd_A Recombination protein RECR; helix-hairpin-helix, zinc finger, toprim, walker B ATP binding motif; 2.50A {Deinococcus radiodurans} SCOP: e.49.1.1 PDB: 2v1c_A

Probab=94.44  E-value=0.018  Score=55.13  Aligned_cols=57  Identities=9%  Similarity=0.050  Sum_probs=45.4

Q ss_pred             ccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEe--------cccCHHHHHHHHHhCCCC
Q psy8714         105 KDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARF--------SAITDKDIKAAMWNLVKP  166 (562)
Q Consensus       105 ~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~--------sslt~~~I~~A~~nl~~~  166 (562)
                      ..+++||+||+|+-|||..++.|.+.++..     ..+|.|+=.        -=++.-.+.+||.+-++.
T Consensus       132 ~~V~EVIlAtnpTvEGEaTA~YI~~~Lk~~-----~vkVTRiA~GiPvGgeLEY~De~TL~~Al~~R~~~  196 (228)
T 1vdd_A          132 GQGMEVILATGTTVEGDATALYLQRLLEPL-----GAAISRIAYGVPVGGSLEYTDEVTLGRALTGRQTV  196 (228)
T ss_dssp             CTTCEEEECCCSSHHHHHHHHHHHHHHTTS-----SCEEEECCBCBCTTCCGGGSCHHHHHHHHHTCEEE
T ss_pred             CCCCEEEEeCCCCchHHHHHHHHHHHHHHc-----CCCEEEecccCCCCcceeeccHHHHHHHHHcCccc
Confidence            578999999999999999999999999643     567888742        335777888888876543

>2fcj_A Small toprim domain protein; structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; HET: MES; 1.30A {Geobacillus stearothermophilus} SCOP: c.136.1.1 PDB: 2i5r_A*

Probab=92.78  E-value=0.15  Score=44.33  Aligned_cols=65  Identities=14%  Similarity=0.007  Sum_probs=45.5

Q ss_pred             hHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCC--CCcEEEEEecccCHHHHHHHHHhCCC
Q psy8714          96 LPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININS--PKTVWRARFSAITDKDIKAAMWNLVK  165 (562)
Q Consensus        96 ~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~--~~~v~Rl~~sslt~~~I~~A~~nl~~  165 (562)
                      .+..|+.+. +-..||+.||||+-||.|-..|.+++... ...+  +.+.   =+..+++++|++|+.+...
T Consensus        40 ~l~~I~~~~-~~r~VIi~TD~D~~GekIRk~i~~~lp~~-~hafi~r~~~---gVE~a~~~~I~~aL~~~~~  106 (119)
T 2fcj_A           40 RLEELADEL-EGYDVYLLADADEAGEKLRRQFRRMFPEA-EHLYIDRAYR---EVAAAPIWHLAQVLLRARF  106 (119)
T ss_dssp             HHHHHHHHT-TTSEEEEECCSSHHHHHHHHHHHHHCTTS-EEECCCTTTC---STTTSCHHHHHHHHHHTTC
T ss_pred             HHHHHHHHh-cCCCEEEEECCCccHHHHHHHHHHHCCCC-cEEeccCCcc---CcccCCHHHHHHHHHhccc
Confidence            344555543 35689999999999999999998887432 0000  1111   3568899999999998764

>1tbx_A ORF F-93, hypothetical 11.0 kDa protein; sulfolobus spindle virus, winged helix, fusellovirus; 2.70A {Sulfolobus virus 1} SCOP: a.4.5.48

Probab=90.07  E-value=0.3  Score=40.13  Aligned_cols=55  Identities=15%  Similarity=0.197  Sum_probs=43.2

Q ss_pred             CCHHHHHHHH-HhcCCCCcCchhHHHHHhhcCCeEEEc---CCCeeecchhHHHHHHhhh
Q psy8714         488 LTESELISLM-EKHGIGTDASIPVHINNICQRNYVTVT---SGRRLVPTSLGIVLVHGYQ  543 (562)
Q Consensus       488 ~Te~~Li~~M-e~~GIGTpATra~iI~~L~~r~Yi~~~---~~k~l~~T~~G~~li~~l~  543 (562)
                      .|..+|.+.| +..|+ +++|-..+|..|.++|||.+.   ..+.+.+|+.|+.+++.+.
T Consensus        23 ~~~~el~~~la~~l~i-s~~tvs~~l~~Le~~gli~r~~~~r~~~~~LT~~G~~~~~~~~   81 (99)
T 1tbx_A           23 IATYDLYKKVNAEFPM-STATFYDAKKFLIQEGFVKERQERGEKRLYLTEKGKLFAISLK   81 (99)
T ss_dssp             CBHHHHHHHHHTTSCC-CHHHHHHHHHHHHHTTSEEEEEETTEEEEEECHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHcCC-CHHHHHHHHHHHHHCCCEEEEecCCceEEEECHHHHHHHHHHH
Confidence            5677776666 55576 678889999999999999862   2346999999999987653

>1t6t_1 Putative protein; structural genomics, PSI, protein structur initiative, midwest center for structural genomics, MCSG, U function; 1.80A {Aquifex aeolicus} SCOP: c.136.1.1

Probab=87.71  E-value=0.5  Score=40.89  Aligned_cols=30  Identities=27%  Similarity=0.364  Sum_probs=26.1

Q ss_pred             cccCCeEEEecCCCccchhHHHHHHHHHhh
Q psy8714         104 AKDCEFLVLWLDCDKEGENICFEVMEAVRH  133 (562)
Q Consensus       104 ~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~  133 (562)
                      .+..+.||+.||||+.||.|...+.+++..
T Consensus        59 ~~~~~~VIIltD~D~aGe~ir~~i~~~l~~   88 (118)
T 1t6t_1           59 EGKWEKVILLFDLDTHGERINQKMKELLSS   88 (118)
T ss_dssp             TTTCSEEEECCCSSHHHHHHHHHHHHHHHH
T ss_pred             HhCCCEEEEEECCChhHHHHHHHHHHhcCc
Confidence            345667999999999999999999999864

>3vdp_A Recombination protein RECR; zinc finger, DNA repair, DNA binding; 2.45A {Thermoanaerobacter tengcongensis} PDB: 3vdu_A 3ve5_D

Probab=87.00  E-value=0.47  Score=45.06  Aligned_cols=54  Identities=15%  Similarity=0.078  Sum_probs=41.2

Q ss_pred             ccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEe--------cccCHHHHHHHHHhC
Q psy8714         105 KDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARF--------SAITDKDIKAAMWNL  163 (562)
Q Consensus       105 ~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~--------sslt~~~I~~A~~nl  163 (562)
                      .++++||+||+|.-|||.-+..|.+.++..     ..+|.|+=.        -=+++-.+.+||.+-
T Consensus       148 ~~v~EVIlAtnpTvEGeaTa~Yi~~~Lk~~-----~vkvTRiA~GiPvGgeLEY~D~~TL~~Al~~R  209 (212)
T 3vdp_A          148 GSVKEVILATNPDIEGEATAMYIAKLLKPF-----GVKVTRIAHGIPVGGDLEYTDVVTLSKALEGR  209 (212)
T ss_dssp             SCCSEEEECCCSSHHHHHHHHHHHHHHTTT-----TCEEEECCBSBCTTCCGGGSCHHHHHHHHHTC
T ss_pred             CCCcEEEEECCCCccHHHHHHHHHHHhhhc-----CCCeeeccccCcCCcchhhccHHHHHHHHHhC
Confidence            468999999999999999999999999643     467777632        234566677777654

>1r7j_A Conserved hypothetical protein SSO10A; winged helix-turn-helix, two-stranded antiparallel coiled CO structural genomics, PSI; 1.47A {Sulfolobus solfataricus} SCOP: a.4.5.49 PDB: 1xsx_A

Probab=84.52  E-value=0.55  Score=38.84  Aligned_cols=43  Identities=16%  Similarity=0.169  Sum_probs=33.4

Q ss_pred             cCCCCcCchhHHHHHhhcCCeEEEcCCCeeecchhHHHHHHhhhc
Q psy8714         500 HGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQK  544 (562)
Q Consensus       500 ~GIGTpATra~iI~~L~~r~Yi~~~~~k~l~~T~~G~~li~~l~~  544 (562)
                      .|+. +++-...++.|.+.|||+.. ...+..|++|+.+++.++.
T Consensus        30 ~~ls-~~~~~~~l~~L~~~GLI~~~-~~~~~LT~kG~~~l~~l~~   72 (95)
T 1r7j_A           30 ANLS-YALTGRYIKMLMDLEIIRQE-GKQYMLTKKGEELLEDIRK   72 (95)
T ss_dssp             HTCC-HHHHHHHHHHHHHTTSEEEE-TTEEEECHHHHHHHHHHHH
T ss_pred             hCcC-HHHHHHHHHHHHHCCCeEEE-CCeeEEChhHHHHHHHHHH
Confidence            3443 44455789999999999984 4479999999999887754

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	562
d1mw9x_	591	e.10.1.1 (X:) DNA topoisomerase I, 67K N-terminal	1e-85
d1i7da_	620	e.10.1.1 (A:) DNA topoisomerase III {Escherichia c	2e-72
d1gkub3	556	e.10.1.1 (B:499-1054) Topoisomerase "domain" of re	2e-57
d1cy9a_	260	e.10.1.1 (A:) DNA topoisomerase I, 67K N-terminal	1e-28

>d1mw9x_ e.10.1.1 (X:) DNA topoisomerase I, 67K N-terminal domain {Escherichia coli [TaxId: 562]} Length = 591

class: Multi-domain proteins (alpha and beta)
fold: Prokaryotic type I DNA topoisomerase
superfamily: Prokaryotic type I DNA topoisomerase
family: Prokaryotic type I DNA topoisomerase
domain: DNA topoisomerase I, 67K N-terminal domain
species: Escherichia coli [TaxId: 562]

 Score =  275 bits (704), Expect = 1e-85
 Identities = 116/507 (22%), Positives = 190/507 (37%), Gaps = 26/507 (5%)

Query: 58  GHIMGLDFTSKYNNWDKVDPLELFSCPTEKREATPKLKLPAFLANEAKDCEFLVLWLDCD 117
                 D      N   VDP   +    E      K K+ + L   A+  + + L  D D
Sbjct: 55  AKKPKKDERGALVNRMGVDPWHNWEAHYEVLPG--KEKVVSELKQLAEKADHIYLATDLD 112

Query: 118 KEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNLVKPNIFEARSVDAR 177
           +EGE I + + E +             R  F+ IT   I+ A     + NI    +  AR
Sbjct: 113 REGEAIAWHLREVIG-----GDDARYSRVVFNEITKNAIRQAFNKPGELNIDRVNAQQAR 167

Query: 178 QELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYW 237
           + +D  +G   +    K             +S G  Q+  +   VER  +I+ F PE +W
Sbjct: 168 RFMDRVVGYMVSPLLWKKIARG--------LSAGRVQSVAVRLVVEREREIKAFVPEEFW 219

Query: 238 LLDLTLNLNG---VAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSK--TK 292
            +D +        +A+ VT      F          AV   +      ++   K      
Sbjct: 220 EVDASTTTPSGEALALQVTHQNDKPFRPVNKEQTQAAVSLLEKARYSVLEREDKPTTSKP 279

Query: 293 PQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENFDLVAVLRQQ 352
                T  L + AS+ LG G    M +A+RLY  GY++Y RT++T   +  D V ++R  
Sbjct: 280 GAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYITYMRTDSTNLSQ--DAVNMVRGY 337

Query: 353 ESSPDWGDHVREVLSNGISKPRKGKDVGDHPPITPTKLATR-TQLDGDAWRLYDYIVRHF 411
            S      ++ E  +   SK    +      P     +A     ++ DA +LY  I R F
Sbjct: 338 ISDNFGKKYLPESPNQYASKENSQEAREAIRPSDVNVMAESLKDMEADAQKLYQLIWRQF 397

Query: 412 IGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSA--MKNESIPDFKPGDL 469
           +        Y          D       + L   G+T VM       ++  +P    GD 
Sbjct: 398 VACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKGDEDRILPAVNKGDA 457

Query: 470 IPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGRRL 529
           + +  +   +  T PP   +E+ L+  +EK GIG  ++    I+ I  R YV V   RR 
Sbjct: 458 LTLVELTPAQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRV-ENRRF 516

Query: 530 VPTSLGIVLVHGYQKIDRELVEPTMRS 556
               +G ++    ++  REL+     +
Sbjct: 517 YAEKMGEIVTDRLEENFRELMNYDFTA 543

>d1i7da_ e.10.1.1 (A:) DNA topoisomerase III {Escherichia coli [TaxId: 562]} Length = 620

class: Multi-domain proteins (alpha and beta)
fold: Prokaryotic type I DNA topoisomerase
superfamily: Prokaryotic type I DNA topoisomerase
family: Prokaryotic type I DNA topoisomerase
domain: DNA topoisomerase III
species: Escherichia coli [TaxId: 562]

 Score =  241 bits (614), Expect = 2e-72
 Identities = 104/547 (19%), Positives = 200/547 (36%), Gaps = 51/547 (9%)

Query: 51  FKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPTEKREATP---KLKLPAFLANEAKDC 107
             +T   GH++       Y++      L       EK +  P     K    +     + 
Sbjct: 36  QVVTWCIGHLLEQAQPDAYDSRYARWNLADLPIVPEKWQLQPRPSVTKQLNVIKRFLHEA 95

Query: 108 EFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNLVKPN 167
             +V   D D+EG+ +  EV++ ++  +     + V R   + +  + ++ A+  L   +
Sbjct: 96  SEIVHAGDPDREGQLLVDEVLDYLQ--LAPEKRQQVQRCLINDLNPQAVERAIDRLRSNS 153

Query: 168 IFEARSVDA--RQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERH 225
            F    V A  R   D   G   TR  T   +         ++S G  QTP LG  V R 
Sbjct: 154 EFVPLCVSALARARADWLYGINMTRAYTILGRNAGYQ---GVLSVGRVQTPVLGLVVRRD 210

Query: 226 DKIRTFKPEPYWLLDLTLNLNGVA------------VSVTWSRGHIFDKSTCNVFFKAVE 273
           ++I  F  + ++ +   +                         G +  +         + 
Sbjct: 211 EEIENFVAKDFFEVKAHIVTPADERFTAIWQPSEACEPYQDEEGRLLHRPLAEHVVNRIS 270

Query: 274 KEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQ-GYVSYP 332
            +  + V       +S++ P   +   L   A+   G+   + + I ++LY     +++P
Sbjct: 271 GQPAI-VTSYNDKRESESAPLPFSLSALQIEAAKRFGLSAQNVLDICQKLYETHKLITFP 329

Query: 333 RTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPR--KGKDVGDHPPITPTKL 390
           R++    PE             S    D + + + +   + R    K V  H  I PT  
Sbjct: 330 RSDCRYLPEEHFAGRHAVMNAISVHAPDLLPQPVVDPDIRNRCWDDKKVDAHHAIIPTAR 389

Query: 391 ATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTG- 449
           ++   L  +  ++Y+ I R ++   C D V+ + V +  +A   F  +A++L   G+   
Sbjct: 390 SSAINLTENEAKVYNLIARQYLMQFCPDAVFRKCVIELDIAKGKFVAKARFLAEAGWRTL 449

Query: 450 ---VMTWSAMKNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLME-------- 498
                         +P    GD +  +  ++VER+T PP + T++ L+S M         
Sbjct: 450 LGSKERDEENDGTPLPVVAKGDELLCEKGEVVERQTQPPRHFTDATLLSAMTGIARFVQD 509

Query: 499 ---------KHGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDREL 549
                      G+GT+A+    I  + +R ++T   GR +  T  G  L H   +     
Sbjct: 510 KDLKKILRATDGLGTEATRAGIIELLFKRGFLTK-KGRYIHSTDAGKALFHSLPE---MA 565

Query: 550 VEPTMRS 556
             P M +
Sbjct: 566 TRPDMTA 572

>d1gkub3 e.10.1.1 (B:499-1054) Topoisomerase "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Length = 556

class: Multi-domain proteins (alpha and beta)
fold: Prokaryotic type I DNA topoisomerase
superfamily: Prokaryotic type I DNA topoisomerase
family: Prokaryotic type I DNA topoisomerase
domain: Topoisomerase "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

 Score =  199 bits (506), Expect = 2e-57
 Identities = 101/536 (18%), Positives = 181/536 (33%), Gaps = 69/536 (12%)

Query: 41  VGPLFGDLVLFKMTSVCGHIMGL-------------DFTSKYNNWDKVDPLELF------ 81
           V  +     +  +T+  GH++ L              F   Y +  +             
Sbjct: 39  VYEIPMQKYVLMVTASIGHVVDLITNRGFHGVLVNGRFVPVYASIKRCRDCGYQFTEDRE 98

Query: 82  SCPTEKREATP-KLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSP 140
           SCP    E           L   A D EF+++  D D EGE I +++         ++  
Sbjct: 99  SCPKCGSENVDNSRSRIEALRKLAHDAEFVIVGTDPDTEGEKIAWDLKNL------LSGC 152

Query: 141 KTVWRARFSAITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKY 200
             V RA F  +T + I  A+ +L   +    ++   R+  D  IG   ++   + F  + 
Sbjct: 153 GAVKRAEFHEVTRRAILEALESLRDVDENLVKAQVVRRIEDRWIGFVLSQKLWERFNNRN 212

Query: 201 GDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSRGHIF 260
                  +S G  QT  LG+ ++R  + R  +                           F
Sbjct: 213 -------LSAGRAQTLVLGWIIDRFQESRERRKIAIV--------------------RDF 245

Query: 261 DKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIA 320
           D        +  E+E  +T+  V+   + +T      T  ++  A+  L       MQIA
Sbjct: 246 DL-----VLEHDEEEFDLTIKLVEEREELRTPLPPYTTETMLSDANRILKFSVKQTMQIA 300

Query: 321 ERLYTQGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVG 380
           + L+  G ++Y RT++T+  +    +A     +                I   R      
Sbjct: 301 QELFENGLITYHRTDSTRVSDVGQRIAKEYLGDDFVGREWGESG-AHECIRPTRPLTRDD 359

Query: 381 DHPPITPTKLATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAK 440
               I    L     L  + + LYD I R F+ + C       K        +    E  
Sbjct: 360 VQRLIQEGVLVV-EGLRWEHFALYDLIFRRFMASQCRPFKVVVKKYSIEFDGKTAEEE-- 416

Query: 441 YLLHPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKH 500
            ++         + A+  +   +   G       VK            T+SE+I +M++ 
Sbjct: 417 RIVRAEGRAYELYRAVWVK--NELPTGTFRVKAEVK----SVPKVLPFTQSEIIQMMKER 470

Query: 501 GIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRS 556
           GIG  ++    ++ +  RNYV      R++PT LGI +     +   + V      
Sbjct: 471 GIGRPSTYATIVDRLFMRNYVVE-KYGRMIPTKLGIDVFRFLVRRYAKFVSEDRTR 525

>d1cy9a_ e.10.1.1 (A:) DNA topoisomerase I, 67K N-terminal domain {Escherichia coli [TaxId: 562]} Length = 260

class: Multi-domain proteins (alpha and beta)
fold: Prokaryotic type I DNA topoisomerase
superfamily: Prokaryotic type I DNA topoisomerase
family: Prokaryotic type I DNA topoisomerase
domain: DNA topoisomerase I, 67K N-terminal domain
species: Escherichia coli [TaxId: 562]

 Score =  112 bits (280), Expect = 1e-28
 Identities = 56/266 (21%), Positives = 99/266 (37%), Gaps = 18/266 (6%)

Query: 231 FKPEPYWLLDLTLNLNG---VAVSVTWSRGH---IFDKSTCNVFFKAVEKEKHVTVVDVQ 284
           F PE +W +D +        +A+ VT          +K         +EK ++ +V++ +
Sbjct: 1   FVPEEFWEVDASTTTPSGEALALQVTHQNDKPFRPVNKEQTQAAVSLLEKARY-SVLERE 59

Query: 285 SSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENFD 344
               +        T  L + AS+ LG G    M +A+RLY  GY++Y RT++T   ++  
Sbjct: 60  DKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYITYMRTDSTNLSQDAV 119

Query: 345 LVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVGDHPPITPTKLATR----TQLDGDA 400
            +    +   S ++G        +      K      H  I P+ +         ++ DA
Sbjct: 120 NMV---RGYISDNFGKKYLPE--SPNQYASKENSQEAHEAIRPSDVNVMAESLKDMEADA 174

Query: 401 WRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNES 460
            +LY  I R F+        Y          D       + L   G+T VM      +E 
Sbjct: 175 QKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKGDED 234

Query: 461 --IPDFKPGDLIPIQSVKMVERKTTP 484
             +P    GD + +  +   +  T P
Sbjct: 235 RILPAVNKGDALTLVELTPAQHFTKP 260

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	562
d1i7da_	620	DNA topoisomerase III {Escherichia coli [TaxId: 56	100.0
d1mw9x_	591	DNA topoisomerase I, 67K N-terminal domain {Escher	100.0
d1gkub3	556	Topoisomerase "domain" of reverse gyrase {Archaeon	100.0
d1cy9a_	260	DNA topoisomerase I, 67K N-terminal domain {Escher	100.0
d1vdda_	199	Recombination protein RecR {Deinococcus radioduran	93.04
d1mw9x_	591	DNA topoisomerase I, 67K N-terminal domain {Escher	87.31
d1q1ha_	88	Transcription factor E/IIe-alpha, N-terminal domai	86.56
d1r7ja_	90	Sso10a (SSO10449) {Archaeon Sulfolobus solfataricu	83.17
d1jgsa_	138	Multiple antibiotic resistance repressor, MarR {Es	81.6
d2bv6a1	136	Transcriptional regulator MgrA {Staphylococcus aur	80.11

>d1i7da_ e.10.1.1 (A:) DNA topoisomerase III {Escherichia coli [TaxId: 562]}

class: Multi-domain proteins (alpha and beta)
fold: Prokaryotic type I DNA topoisomerase
superfamily: Prokaryotic type I DNA topoisomerase
family: Prokaryotic type I DNA topoisomerase
domain: DNA topoisomerase III
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=2.5e-124  Score=1047.64  Aligned_cols=532  Identities=21%  Similarity=0.336  Sum_probs=445.0

Q ss_pred             eEEEEecccCcCCcchHHhhcccccCCCCceeeeeeeeEc-CCCcEEEEEEecccccccccccC----CCCCccCCCCCC
Q psy8714           6 KKLVPASEIKLARPSLISLLTPLQRMNGACSVHEWVGPLF-GDLVLFKMTSVCGHIMGLDFTSK----YNNWDKVDPLEL   80 (562)
Q Consensus         6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~~~~~~~~~g~~~-g~~~~~~Vt~~~GHl~~l~~~~~----y~~W~~~~p~~~   80 (562)
                      |+||||||     ||+|+.|++++|....    .-+||++ |++  |+||||.|||++|++|++    |+.|+..++. +
T Consensus         1 MkLiIaEk-----Ps~Ak~Ia~~Lg~~~~----~~~g~~~~g~~--~~Vt~~~GHl~~l~~p~~~~~~~~~w~~~~lp-~   68 (620)
T d1i7da_           1 MRLFIAEK-----PSLARAIADVLPKPHR----KGDGFIECGNG--QVVTWCIGHLLEQAQPDAYDSRYARWNLADLP-I   68 (620)
T ss_dssp             CEEEEESS-----HHHHHHHHTTSCSCCE----EETTEEEETTT--EEEEECSSCSEEECCHHHHCGGGGSCCSTTCS-C
T ss_pred             CeEEEECC-----HHHHHHHHHHhCCccc----cCCCceecCCC--eEEEEeCCcCcCCCCchhccccccCCccccCC-C
Confidence            78999999     9999999999986532    3467887 553  899999999999976654    5678765521 2


Q ss_pred             CCCCcccccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHHHH
Q psy8714          81 FSCPTEKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAM  160 (562)
Q Consensus        81 ~~~~~~~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~A~  160 (562)
                      .+............++++.|++++++||+||||||||||||+|||||+++|+...  +.+++|+|+|||++|+++|++||
T Consensus        69 ~p~~~~~~~~~~~~k~~~~lk~l~k~ad~iilAtD~DREGE~Ia~~i~~~~~~~~--~~~~~v~R~~f~~iT~~aI~~A~  146 (620)
T d1i7da_          69 VPEKWQLQPRPSVTKQLNVIKRFLHEASEIVHAGDPDREGQLLVDEVLDYLQLAP--EKRQQVQRCLINDLNPQAVERAI  146 (620)
T ss_dssp             CCSSCCEEECGGGHHHHHHHHHHHHHCSEEEEECCSSHHHHHHHHHHHHHTTCCH--HHHHTCEECCCSCCSHHHHHHHH
T ss_pred             CCccceeeeCccHHHHHHHHHHHHhcCCEEEEcCCCCcchhHHHHHHHHHhcccc--ccCCceEEEEeecCcHHHHHHHH
Confidence            2211111111223467888888899999999999999999999999999995310  11478999999999999999999


Q ss_pred             HhCCCCh--HhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhhhhhhhhhhcccCcceEE
Q psy8714         161 WNLVKPN--IFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWL  238 (562)
Q Consensus       161 ~nl~~~~--~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lIv~Re~eI~~F~p~~y~~  238 (562)
                      +|+++++  .++++||.||+++||+||||+||++|++++..+.   .+++|+||||||||+|||+||++|++|+|++||.
T Consensus       147 ~n~~~~~~~~~l~~a~~aR~~~D~liG~~~Sr~~t~~~~~~~~---~~~lS~GRVQtPtL~lIveRe~eI~~F~p~~y~~  223 (620)
T d1i7da_         147 DRLRSNSEFVPLCVSALARARADWLYGINMTRAYTILGRNAGY---QGVLSVGRVQTPVLGLVVRRDEEIENFVAKDFFE  223 (620)
T ss_dssp             TTCEEGGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTC---CSCCCCCTTHHHHHHHHHHHHHHHHTCCCCEEEE
T ss_pred             HhcCCchhhhhHHHHHHHhHHHHhhcCcchhHHHHHHHhhcCC---CccccccccccchhhhHHHHHHHHhhccccceee
Confidence            9999988  4789999999999999999999999988765332   3579999999999999999999999999999999


Q ss_pred             EEEEEeeC-CeEEEEEee-----------cccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHHHHHHHHH
Q psy8714         239 LDLTLNLN-GVAVSVTWS-----------RGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVAS  306 (562)
Q Consensus       239 i~~~~~~~-~~~~~~~~~-----------~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~  306 (562)
                      |.+.|... +..|.+.|.           ++++.+++.|+.+++.+.+ ..++|.+++.++++.+||+||+|++||++||
T Consensus       224 i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~-~~~~V~~v~~k~~~~~pP~Pf~ts~LQ~~As  302 (620)
T d1i7da_         224 VKAHIVTPADERFTAIWQPSEACEPYQDEEGRLLHRPLAEHVVNRISG-QPAIVTSYNDKRESESAPLPFSLSALQIEAA  302 (620)
T ss_dssp             EEEEEECTTCCEEEEEECCCGGGTTTBCTTCCBCCHHHHHHHHHHHSS-CEEECCEEEEEEEEECCCCSBCHHHHHHHHH
T ss_pred             eeeEeccccchhhhhhhcccccccccchhhhhHhHHHHHHHHHHHhcc-CCeEEEEecccceecCCCcccchHHHHHHhh
Confidence            99999754 456777773           4578899999999999976 4789999999999999999999999999999


Q ss_pred             hhCCCCHHHHHHHHHHhHhc-CceeecCCCCCCCCCcc--cHHHHHHHhccC-CchhHHHHHHhhCCCCCCC--CCCCCC
Q psy8714         307 SGLGMGPHHAMQIAERLYTQ-GYVSYPRTETTQYPENF--DLVAVLRQQESS-PDWGDHVREVLSNGISKPR--KGKDVG  380 (562)
Q Consensus       307 ~~~g~s~~~tl~iaQ~LYE~-glISYPRTds~~l~~~~--~~~~~l~~l~~~-~~~~~~~~~~~~~~~~~~~--~~~~~~  380 (562)
                      ++|||||++||++||+|||+ ||||||||||++||+++  .+..++..+... ..+..  ..... .....+  ++++++
T Consensus       303 ~~lg~s~~~tm~iAQ~LYe~~glITYpRTDS~~ls~~~~~~~~~~~~~~~~~~~~~~~--~~~~~-~~~~~~~~~~~~~~  379 (620)
T d1i7da_         303 KRFGLSAQNVLDICQKLYETHKLITFPRSDCRYLPEEHFAGRHAVMNAISVHAPDLLP--QPVVD-PDIRNRCWDDKKVD  379 (620)
T ss_dssp             HHHCCCHHHHHHHHHHHHHTSCCBSCSSCCCCCBCGGGGGGHHHHHHHHHHHSTTTCC--CTTCC-TTCCCTTBCGGGCC
T ss_pred             hhcCCcHHHHHHHHHHHHHhcCceecccCccccCcHHHHHHHHHHHHHhhcccccccc--ccccc-ccccccccCCcccC
Confidence            99999999999999999997 99999999999999875  244444443211 11100  00000 001112  223457


Q ss_pred             CCCCCccCCCcccCCCCHHHHHHHHHHHHHHHhhcccCceEEEEEEEEEECCeEEEEEEEEEeecceeeeecccccc---
Q psy8714         381 DHPPITPTKLATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMK---  457 (562)
Q Consensus       381 ~H~AI~PT~~~~~~~L~~~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~v~~~~~~~---  457 (562)
                      +||||+||...+...|+++|++||+||||||||+||+||+|++|++.+.++++.|.++|++++++||+.+|+.+...   
T Consensus       380 aH~aI~Pt~~~~~~~l~~~e~klY~LI~~r~las~~~~a~~~~t~~~~~~~~~~F~~~g~~i~~~Gw~~v~~~~~~~~~~  459 (620)
T d1i7da_         380 AHHAIIPTARSSAINLTENEAKVYNLIARQYLMQFCPDAVFRKCVIELDIAKGKFVAKARFLAEAGWRTLLGSKERDEEN  459 (620)
T ss_dssp             SSCCBCBCSCCSCCCCCHHHHHHHHHHHHHHHHTTSCCEEEEEEEEEECSTTCCEEECEEEEEECGGGGGSCTTGGGTTC
T ss_pred             CcccccccchhhccCCCHHHHHHHHHHHHHHHHhhCcchhccceEEEEEeccccccccccccccCceeeeecccccchhc
Confidence            89999999876666899999999999999999999999999999999999999999999999999999999754332   


Q ss_pred             -cCCCCCCCCCCeeeeeeeEEeeeecCCCCCCCHHHHHHHHHh-----------------cCCCCcCchhHHHHHhhcCC
Q psy8714         458 -NESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEK-----------------HGIGTDASIPVHINNICQRN  519 (562)
Q Consensus       458 -~~~Lp~l~~G~~~~~~~~~i~e~~TkPP~~~Te~~Li~~Me~-----------------~GIGTpATra~iI~~L~~r~  519 (562)
                       +..||.+++|+.+.+.++.+.+++|+||+||||++||++||+                 +|||||||||+||++|++||
T Consensus       460 ~~~~lp~l~~g~~~~~~~~~~~e~~T~PP~ryTEasLi~~Me~~~k~~~d~~l~~~l~~~~GIGtpaT~a~iI~~L~~R~  539 (620)
T d1i7da_         460 DGTPLPVVAKGDELLCEKGEVVERQTQPPRHFTDATLLSAMTGIARFVQDKDLKKILRATDGLGTEATRAGIIELLFKRG  539 (620)
T ss_dssp             EECCCCCCCTTCEEEEEEEEEEEEECCCCCCEEHHHHHHHHHTGGGGCCCHHHHHHHHHTTSSSCTTTHHHHHHHHHHTT
T ss_pred             ccccccccccCCeecccccccccccCCCCCCCCHHHHHHHHHhhccccccHHHHHhhcccCCCCccccHHHHHHHHHhCC
Confidence             356999999999999999999999999999999999999984                 59999999999999999999


Q ss_pred             eEEEcCCCeeecchhHHHHHHhhhccCccCCChhhHHHHHhhC
Q psy8714         520 YVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRVQA  562 (562)
Q Consensus       520 Yi~~~~~k~l~~T~~G~~li~~l~~~~~~l~~p~~Ta~~E~~L  562 (562)
                      ||.. +|++|+||++|+.|+++|   +..+++|+|||.||.+|
T Consensus       540 Yv~~-~~k~l~pT~~G~~l~~~l---~~~~~~~~~Ta~~E~~L  578 (620)
T d1i7da_         540 FLTK-KGRYIHSTDAGKALFHSL---PEMATRPDMTAHWESVL  578 (620)
T ss_dssp             SEEE-SSSEEEECHHHHHHHHHS---CHHHHSTHHHHHHHHHH
T ss_pred             cEEe-cCCEEeecHHHHHHHHHH---HHhcCCHhHHHHHHHHH
Confidence            9998 788999999999999986   45689999999999875

>d1mw9x_ e.10.1.1 (X:) DNA topoisomerase I, 67K N-terminal domain {Escherichia coli [TaxId: 562]}

class: Multi-domain proteins (alpha and beta)
fold: Prokaryotic type I DNA topoisomerase
superfamily: Prokaryotic type I DNA topoisomerase
family: Prokaryotic type I DNA topoisomerase
domain: DNA topoisomerase I, 67K N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=1e-118  Score=998.85  Aligned_cols=508  Identities=22%  Similarity=0.322  Sum_probs=425.6

Q ss_pred             eEEEEecccCcCCcchHHhhcccccCCCCceeeeeeeeEcCCCcEEEEEEecccccccccccCCC----CCccCC-----
Q psy8714           6 KKLVPASEIKLARPSLISLLTPLQRMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYN----NWDKVD-----   76 (562)
Q Consensus         6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~~~~~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~~~~y~----~W~~~~-----   76 (562)
                      |+||||||     ||+|+.|+.++|                ++  |+|+||+|||++|..|+.|.    .|...+     
T Consensus         2 K~LiIaEK-----Ps~Ak~Ia~~Lg----------------~~--y~V~~~~GHl~~l~~~~~~~~~~~~~~~~~~~~~~   58 (591)
T d1mw9x_           2 KALVIVES-----PAKAKTINKYLG----------------SD--YVVKSSVGHIRDLPTSGSAAKKSADSTSTKTAKKP   58 (591)
T ss_dssp             CEEEEESC-----HHHHHHHHTTSC----------------TT--EEEEECCSCCEESCC--------------------
T ss_pred             CEEEEECC-----HHHHHHHHHHhC----------------CC--CEEEeccCceeECCCCccccccccccccccccccc
Confidence            79999999     999999997654                22  68999999999998777653    444321     


Q ss_pred             ---------------CCCCCCCCcccccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCC
Q psy8714          77 ---------------PLELFSCPTEKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPK  141 (562)
Q Consensus        77 ---------------p~~~~~~~~~~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~  141 (562)
                                     |...|...  ......+.++++.|++++++||+||||||||||||+|||+|+++++.     .++
T Consensus        59 ~~~~~~~~~~~~~~~p~~~~~~~--~~~~~~~~k~~~~ik~l~k~~d~iiiAtD~DrEGE~I~~~i~~~~~~-----~~~  131 (591)
T d1mw9x_          59 KKDERGALVNRMGVDPWHNWEAH--YEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGG-----DDA  131 (591)
T ss_dssp             ---CHHHHHHHHTEETTTTTEEC--CEECTTCHHHHHHHHHHHHTCSEEEECCCSSHHHHHHHHHHHHHHCS-----CGG
T ss_pred             ccccccccccccCcCcccCCcee--EEECCchHHHHHHHHHHHhcCCEEEECCCCCccchHHHHHHHHHhcc-----CCC
Confidence                           11111100  11122345688889999999999999999999999999999999853     356


Q ss_pred             cEEEEEecccCHHHHHHHHHhCCCChHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhh
Q psy8714         142 TVWRARFSAITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFC  221 (562)
Q Consensus       142 ~v~Rl~~sslt~~~I~~A~~nl~~~~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lI  221 (562)
                      +++|+|||++|+++|++||+|+.+.++++++||.||+++||+||||+||++|+.++        ..+|+||||||||+||
T Consensus       132 ~~~R~~~~~lt~~~i~~A~~n~~~~~~~l~~a~~aR~~~D~liG~n~Sr~~t~~~~--------~~lS~GRVQtPtL~lI  203 (591)
T d1mw9x_         132 RYSRVVFNEITKNAIRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVSPLLWKKIA--------RGLSAGRVQSVAVRLV  203 (591)
T ss_dssp             GEEECCCSSCSHHHHHHHHHSCBCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTC--------TTCCCCTTHHHHHHHH
T ss_pred             ceEEEEeccCCHHHHHHHHhCcccccchHHHHHHHHHHHHHHHHHhcchHHhhhhc--------cccccchhcCcceeee
Confidence            89999999999999999999999999999999999999999999999999998654        2499999999999999


Q ss_pred             hhhhhhhhcccCcceEEEEEEEeeCCeEEEEEee------cccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCC
Q psy8714         222 VERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWS------RGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQA  295 (562)
Q Consensus       222 v~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~------~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~p  295 (562)
                      |+||++|++|+|++||.|.+.+..+++.+.+.|.      ..++.+++.+.+....+.. ..++|++++.++++.+||+|
T Consensus       204 v~Re~ei~~f~p~~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~v~~~~~k~~~~~pP~p  282 (591)
T d1mw9x_         204 VEREREIKAFVPEEFWEVDASTTTPSGEALALQVTHQNDKPFRPVNKEQTQAAVSLLEK-ARYSVLEREDKPTTSKPGAP  282 (591)
T ss_dssp             HHHHHHHHHCCCCEEEEEEEEEECTTCCEEEEEEEEETTEECCCCSHHHHHHHHHHHHH-CCEEEEEEEEEEEEECCCCC
T ss_pred             ehhHHHHHhcCCccccceeeeeecCCcchhhhhhccccccccchhhHHHHHHHHhhhhh-hhhhhccccccccccCCCCC
Confidence            9999999999999999999999987777766553      2367788898888888876 47899999999999999999


Q ss_pred             CCHHHHHHHHHhhCCCCHHHHHHHHHHhHhcCceeecCCCCCCCCCcc--cHHHHHHHhccCCchhHHHHHHhhCCCCCC
Q psy8714         296 LNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENF--DLVAVLRQQESSPDWGDHVREVLSNGISKP  373 (562)
Q Consensus       296 f~l~~Lq~~a~~~~g~s~~~tl~iaQ~LYE~glISYPRTds~~l~~~~--~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~  373 (562)
                      |+|++||++||++|||||++||++||+|||+|+||||||||++||+++  .+.+.|..+..     .   .+.... ...
T Consensus       283 f~l~~Lq~~a~~~~g~s~~~tl~iaQ~LYE~g~ITYPRTds~~l~~~~~~~~~~~i~~~~~-----~---~~~~~~-~~~  353 (591)
T d1mw9x_         283 FITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYITYMRTDSTNLSQDAVNMVRGYISDNFG-----K---KYLPES-PNQ  353 (591)
T ss_dssp             BCHHHHHHHHHHHHCCCHHHHHHHHHHHHHTTSBCCSCCCCCCCCHHHHHHHHHHHHHHTC-----G---GGSCSS-CCC
T ss_pred             ccHHHHHHHHHHHhCCCHHHHHHHHHHHhhCCeeeecccCcccccHHHHHHHHHHHHHHhh-----h---hhhhcc-ccc
Confidence            999999999999999999999999999999999999999999999876  34455544321     1   111111 111


Q ss_pred             CCCC--CCCCCCCCccCCCc----ccCCCCHHHHHHHHHHHHHHHhhcccCceEEEEEEEEEECCeEEEEEEEEEeecce
Q psy8714         374 RKGK--DVGDHPPITPTKLA----TRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGF  447 (562)
Q Consensus       374 ~~~~--~~~~H~AI~PT~~~----~~~~L~~~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw  447 (562)
                      +..+  ...+|+||+||...    +...|+.+|++||+||+|||||+||+|++|+.+++++.++++.|+++|++++++||
T Consensus       354 ~~~~~~~~~ah~~~~~~~~~~~~~~~~~~~~~e~kvY~LI~rrflas~~~~a~~~~t~~~~~~~~~~F~a~g~~~~~~Gw  433 (591)
T d1mw9x_         354 YASKENSQEAREAIRPSDVNVMAESLKDMEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGW  433 (591)
T ss_dssp             CC--------CCCBCBSCTTCCGGGCSSCCHHHHHHHHHHHHHHHHHTSCCEEEEEEEEEEEETTEEEEEEEEEEEECGG
T ss_pred             cccccccccccccccccCccccccchhhcChHHHHHHHHHHHHHHHhccCCeEEEEEEEEeeecCcEEEEEEEEEEecCc
Confidence            1122  23679999999642    34679999999999999999999999999999999999999999999999999999


Q ss_pred             eeeecccccc--cCCCCCCCCCCeeeeeeeEEeeeecCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEcC
Q psy8714         448 TGVMTWSAMK--NESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTS  525 (562)
Q Consensus       448 ~~v~~~~~~~--~~~Lp~l~~G~~~~~~~~~i~e~~TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~~  525 (562)
                      +.+|+.....  +..||.+++|+.+.+.++.+.+++|+||+||||++||++||+.|||||||||+||++|++||||.+ +
T Consensus       434 ~~v~~~~~~~~~~~~lp~l~~g~~~~~~~~~~~e~~TkPP~~yTeatLi~~ME~~GIGTpATra~iIe~L~~R~Yi~~-~  512 (591)
T d1mw9x_         434 TKVMPALRKGDEDRILPAVNKGDALTLVELTPAQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRV-E  512 (591)
T ss_dssp             GGGSCCC----CCCCCCCCCTTCEEEEEEEEEEEEECCCCCCCCHHHHHHHHHHTTCCCTTTHHHHHHHHHHTTSEEE-E
T ss_pred             eEEecccccccccccCCCcCCCCEEEEEEEEEEEeecCCCCCCCHHHHHHHHHhCCCCCcccHHHHHHHHHhCCCEEe-c
Confidence            9999765432  567999999999999999999999999999999999999999999999999999999999999998 6


Q ss_pred             CCeeecchhHHHHHHhhhccCccCCChhhHHHHHhhC
Q psy8714         526 GRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRVQA  562 (562)
Q Consensus       526 ~k~l~~T~~G~~li~~l~~~~~~l~~p~~Ta~~E~~L  562 (562)
                      |++|.||++|+.|+++|....++|++|+|||.||..|
T Consensus       513 ~k~l~pT~~G~~li~~l~~~~~~l~~p~~Ta~~E~~L  549 (591)
T d1mw9x_         513 NRRFYAEKMGEIVTDRLEENFRELMNYDFTAQMENNL  549 (591)
T ss_dssp             TTEEEECHHHHHHHHHHHHHCHHHHCHHHHHHHHHHH
T ss_pred             CCEEeecHHHHHHHHHHHHhhhhhcCHHHHHHHHHHH
Confidence            7899999999999999988788999999999999875

>d1gkub3 e.10.1.1 (B:499-1054) Topoisomerase "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Multi-domain proteins (alpha and beta)
fold: Prokaryotic type I DNA topoisomerase
superfamily: Prokaryotic type I DNA topoisomerase
family: Prokaryotic type I DNA topoisomerase
domain: Topoisomerase "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=100.00  E-value=5.3e-107  Score=899.10  Aligned_cols=486  Identities=21%  Similarity=0.266  Sum_probs=377.4

Q ss_pred             eEEEEecccCcCCcchHHhhcccccCCCCce---eeeeeeeEcCCCcEEEEEEecccccccccccCCC----CCccCC--
Q psy8714           6 KKLVPASEIKLARPSLISLLTPLQRMNGACS---VHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYN----NWDKVD--   76 (562)
Q Consensus         6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~~~~---~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~~~~y~----~W~~~~--   76 (562)
                      +.||||||     ||+|+.||+++|....-+   ...+.|+++  ++.|+||||+|||++|..|++|.    +|+...  
T Consensus         8 ~~LiIaEK-----Ps~ak~Ia~~Lg~~~~k~~~~~~~~~~~~~--~~~~~vt~~~GHl~~L~~p~~~~~~~~~~~~~p~~   80 (556)
T d1gkub3           8 PALFIVES-----PTKARQISRFFGKPSVKVLDGAVVYEIPMQ--KYVLMVTASIGHVVDLITNRGFHGVLVNGRFVPVY   80 (556)
T ss_dssp             EEEEEESC-----HHHHHHHHGGGEECEEEEETTEEEEEEECS--SEEEEEEECCSCSEEECSSSSTTSSCCSSSCCCEE
T ss_pred             CeEEEECC-----HHHHHHHHHHcCCCcccccCCccccccccC--CceEEEEEccCccccCCCcccccccccccCcCccc
Confidence            34999999     999999999998643211   112333443  44789999999999998877663    444210  


Q ss_pred             ----C---C-CCCC-----CC-cccccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCc
Q psy8714          77 ----P---L-ELFS-----CP-TEKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKT  142 (562)
Q Consensus        77 ----p---~-~~~~-----~~-~~~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~  142 (562)
                          +   . ..|.     .+ ..........++++.|++++++||.||||||||||||+|||||+++++      +++|
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~i~~l~k~ad~ii~AtD~DREGE~I~~~i~~~~~------~~~~  154 (556)
T d1gkub3          81 ASIKRCRDCGYQFTEDRESCPKCGSENVDNSRSRIEALRKLAHDAEFVIVGTDPDTEGEKIAWDLKNLLS------GCGA  154 (556)
T ss_dssp             EECC------------------------CCHHHHHHHHHHHHHHHSEEEECCCSSHHHHHHHHHHHHHHT------TSSE
T ss_pred             cccccccccccccccccccccccccccCccHHHHHHHHHHHHhhCCEEEECCCCCcchhHHHHHHHHHhc------CCCC
Confidence                0   0 0010     00 011111233467888999999999999999999999999999999995      3689


Q ss_pred             EEEEEecccCHHHHHHHHHhCCCChHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhhh
Q psy8714         143 VWRARFSAITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCV  222 (562)
Q Consensus       143 v~Rl~~sslt~~~I~~A~~nl~~~~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lIv  222 (562)
                      |+|+|||++|+++|++||+||+++++++++|+.||+++||+||||+||++|..++       ++.+|+||||||||+|||
T Consensus       155 v~R~~~~~~t~~~I~~a~~~l~~~~~~l~~a~~aR~~~D~~iG~~~s~~l~~~~~-------~~~lS~GRVQtPtL~lVv  227 (556)
T d1gkub3         155 VKRAEFHEVTRRAILEALESLRDVDENLVKAQVVRRIEDRWIGFVLSQKLWERFN-------NRNLSAGRAQTLVLGWII  227 (556)
T ss_dssp             EEECCCSBCSHHHHHHHHTSCBCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTT-------CSSCCCCTTHHHHHHHHH
T ss_pred             eEEEEehhccHHHHHhHHhhccccchhhhHHHHHHhHHHHHhcchhHHHHHHHHh-------cccccccccccchhhhhh
Confidence            9999999999999999999999999999999999999999999999999987553       246999999999999999


Q ss_pred             hhhhhhhcccCcceEEEEEEEeeCCeEEEEEeecccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHHHHH
Q psy8714         223 ERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELM  302 (562)
Q Consensus       223 ~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq  302 (562)
                      +|+++|++|++..++.-      .+  ....+.                 .....+.|..++.+++++.||+||+|++||
T Consensus       228 ~Re~ei~~~~~~~~~~~------~~--~~~~~~-----------------~~~~~~~v~~v~~~~~~~~pp~pf~~s~Lq  282 (556)
T d1gkub3         228 DRFQESRERRKIAIVRD------FD--LVLEHD-----------------EEEFDLTIKLVEEREELRTPLPPYTTETML  282 (556)
T ss_dssp             HHHTGGGSEEEEEEETT------TT--EEESCC-----------------CSEEEEEEEEEEEEEEEECCCCCBCHHHHH
T ss_pred             hHHHhhhhccceeeeeh------hh--HHHHHh-----------------hhhccceeeEEEeceEecCCCCCCcchHHH
Confidence            99999999987654421      01  111111                 011246788999999999999999999999


Q ss_pred             HHHHhhCCCCHHHHHHHHHHhHhcCceeecCCCCCCCCCcccHHHHHHHhccCCchhHHHHHHhhCCCCCCCCCCCCCCC
Q psy8714         303 RVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVGDH  382 (562)
Q Consensus       303 ~~a~~~~g~s~~~tl~iaQ~LYE~glISYPRTds~~l~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~H  382 (562)
                      ++||++|||||++||++||+|||+|+||||||||++||+++.  ..+..             .+.. ...........+|
T Consensus       283 ~~a~~~~~~s~~~tl~iaQ~LYe~g~ITYpRTDs~~ls~~~~--~~~~~-------------~~~~-~~~~~~~~~~~~~  346 (556)
T d1gkub3         283 SDANRILKFSVKQTMQIAQELFENGLITYHRTDSTRVSDVGQ--RIAKE-------------YLGD-DFVGREWGESGAH  346 (556)
T ss_dssp             HHHHHTSCCCHHHHHHHHHHHHHTTSBBCSSCCCCCCCHHHH--HHHHH-------------HHTT-SBCCCCSCSCCSC
T ss_pred             HHHhccccccHHHHHHHHhhhhccceeeccCCccccchhhhh--hhhhh-------------hhhh-hcccccccccccc
Confidence            999999999999999999999999999999999999998652  11111             1110 0111122233679


Q ss_pred             CCCccCCCc--------------ccCCCCHHHHHHHHHHHHHHHhhcccCceEEEEEEEEEECCeEEEEEEEEEeeccee
Q psy8714         383 PPITPTKLA--------------TRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFT  448 (562)
Q Consensus       383 ~AI~PT~~~--------------~~~~L~~~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~  448 (562)
                      ++|+||...              +...|+.+|++||+||++||||+||+|++++.+++.+.+++..|...  .+...+|.
T Consensus       347 ~~i~~~~~~~~~d~~~~~~~~~~~~~~l~~~e~~lY~lI~~rflas~~~~~~~~~~~v~~~~~~~~~~~~--~~~~~~~~  424 (556)
T d1gkub3         347 ECIRPTRPLTRDDVQRLIQEGVLVVEGLRWEHFALYDLIFRRFMASQCRPFKVVVKKYSIEFDGKTAEEE--RIVRAEGR  424 (556)
T ss_dssp             CCBCBSSSCCHHHHHHHHHHTCSCCSSCCHHHHHHHHHHHHHHHHTTBCCEEEEEEEEEEEETTEEEEEC--CEEEEESH
T ss_pred             ccccccccccccccccCCCcchhhhccCCHHHHHHhhhhhhhhhHhhcCcceeeEEEEEEeecceeeeee--EEEEeeee
Confidence            999998531              23579999999999999999999999999999999999998766543  33333333


Q ss_pred             eeeccccc-ccCCCCCCCCCCeeeeeeeEEeeeecCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEcCCC
Q psy8714         449 GVMTWSAM-KNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGR  527 (562)
Q Consensus       449 ~v~~~~~~-~~~~Lp~l~~G~~~~~~~~~i~e~~TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~~~k  527 (562)
                      .+..+... .+..+|...       ..+.+++++|+||+||||++||++||+.|||||||||+||++|++||||++ +|+
T Consensus       425 ~~~~~~~~~~~~elp~~~-------~~~~~e~k~t~pp~ryTEasLI~~ME~~GIGTpATrA~IIe~L~~R~Yv~~-k~~  496 (556)
T d1gkub3         425 AYELYRAVWVKNELPTGT-------FRVKAEVKSVPKVLPFTQSEIIQMMKERGIGRPSTYATIVDRLFMRNYVVE-KYG  496 (556)
T ss_dssp             HHHHSCCSCCCCCCCCEE-------EEEEBCCEEEESSCCBCHHHHHHHHHHHTCCCTTTHHHHHHHHHHTTSEEE-ETT
T ss_pred             eeeccchhhhcccccccc-------cccccccccCCCCCCCCHHHHHHHHHhCCCCccccHHHHHHHHHhCCcEEe-eCC
Confidence            33222221 134455432       245667789999999999999999999999999999999999999999998 677


Q ss_pred             eeecchhHHHHHHhhhccCccCCChhhHHHHHhhC
Q psy8714         528 RLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRVQA  562 (562)
Q Consensus       528 ~l~~T~~G~~li~~l~~~~~~l~~p~~Ta~~E~~L  562 (562)
                      +|+||++|+.|+++|...++.|++|+|||.||.+|
T Consensus       497 ~l~pT~~G~~li~~L~~~~~~l~~p~~Ta~~E~~L  531 (556)
T d1gkub3         497 RMIPTKLGIDVFRFLVRRYAKFVSEDRTRDLESRM  531 (556)
T ss_dssp             EEEECHHHHHHHHHHHHSCCGGGSHHHHHHHHHHH
T ss_pred             EEeechHHHHHHHHHHHhhhhhcChHHHHHHHHHH
Confidence            99999999999999998888999999999999976

>d1cy9a_ e.10.1.1 (A:) DNA topoisomerase I, 67K N-terminal domain {Escherichia coli [TaxId: 562]}

class: Multi-domain proteins (alpha and beta)
fold: Prokaryotic type I DNA topoisomerase
superfamily: Prokaryotic type I DNA topoisomerase
family: Prokaryotic type I DNA topoisomerase
domain: DNA topoisomerase I, 67K N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=1.2e-52  Score=420.84  Aligned_cols=245  Identities=21%  Similarity=0.362  Sum_probs=199.3

Q ss_pred             ccCcceEEEEEEEeeCC-eEEEEEe--e---cccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHHHHHHH
Q psy8714         231 FKPEPYWLLDLTLNLNG-VAVSVTW--S---RGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRV  304 (562)
Q Consensus       231 F~p~~y~~i~~~~~~~~-~~~~~~~--~---~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~  304 (562)
                      |+|++||+|.+.|..++ ..|.+.|  .   ..+++++++|+.+++.|++. .++|+++++++++.+||+||||++||++
T Consensus         1 F~p~~yw~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~l~~~-~~~v~~v~~k~~~~~pP~pf~l~~Lq~~   79 (260)
T d1cy9a_           1 FVPEEFWEVDASTTTPSGEALALQVTHQNDKPFRPVNKEQTQAAVSLLEKA-RYSVLEREDKPTTSKPGAPFITSTLQQA   79 (260)
T ss_dssp             CCCCEEEEEEEEEECTTSCEEEEEEEEETTEECCCCSHHHHHHHHHHHHHS-CEEEEEEEEEEEEECCCCCBCHHHHHHH
T ss_pred             CeeCceEEEEEEEEcCCCCEEEEEEeecCCccCCcCCHHHHHHHHHHHhcC-CeEEEEeecccccccCCccccHHHHHHH
Confidence            99999999999998654 4444444  2   34789999999999999874 7899999999999999999999999999


Q ss_pred             HHhhCCCCHHHHHHHHHHhHhcCceeecCCCCCCCCCcc--cHHHHHHHhccCCchhHHHHHHhhCCCCCCCCC-CCCCC
Q psy8714         305 ASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENF--DLVAVLRQQESSPDWGDHVREVLSNGISKPRKG-KDVGD  381 (562)
Q Consensus       305 a~~~~g~s~~~tl~iaQ~LYE~glISYPRTds~~l~~~~--~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~  381 (562)
                      ||++|||||++||++||+|||+|+||||||||++||+++  .+..+|..+.     +..   +........... ....+
T Consensus        80 as~~~g~s~~~tl~iaQ~LYe~g~ITYPRTds~~l~~~~~~~~~~~i~~~~-----~~~---~~~~~~~~~~~~~~~~~~  151 (260)
T d1cy9a_          80 ASTRLGFGVKKTMMMAQRLYEAGYITYMRTDSTNLSQDAVNMVRGYISDNF-----GKK---YLPESPNQYASKENSQEA  151 (260)
T ss_dssp             HHHHHCCCHHHHHHHHHHHHHTTSBCCSCCCCCCCCHHHHHHHHHHHHHHT-----CGG---GSCSSCCCCCC-------
T ss_pred             HHHhcCCCHHHHHHHHHHHHhCCceeecccccccccHHHHHHHHHHHHHHh-----hhh---hcccCcceeccCcccccC
Confidence            999999999999999999999999999999999999986  3555555432     111   111000111111 22367


Q ss_pred             CCCCccCCCc----ccCCCCHHHHHHHHHHHHHHHhhcccCceEEEEEEEEEECCeEEEEEEEEEeecceeeeecccccc
Q psy8714         382 HPPITPTKLA----TRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMK  457 (562)
Q Consensus       382 H~AI~PT~~~----~~~~L~~~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~v~~~~~~~  457 (562)
                      |+||+||...    +...|+.+|++||+||+|||||+|||||+|++|++.+.++++.|+++|++++++||+.+|+....+
T Consensus       152 h~~~~~~~~~~~~~~~~~l~~~e~~iY~lI~~rfla~~~~~~~~~~t~v~~~~~~~~F~a~g~~i~~~Gw~~v~~~~~~~  231 (260)
T d1cy9a_         152 HEAIRPSDVNVMAESLKDMEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKG  231 (260)
T ss_dssp             CCCBCBSCTTCCGGGCTTSCHHHHHHHHHHHHHHHHHTSCCEEEEEEEEEEEETTEEEEEEEEEEEECGGGGTC------
T ss_pred             ccccccccccccccchhhCCHHHHHHHHHHHHHHHHhccCcceeeeeEEeeeeceeEEEEEEEEEEeCChHHHhCccccC
Confidence            9999998642    346899999999999999999999999999999999999999999999999999999999865433


Q ss_pred             --cCCCCCCCCCCeeeeeeeEEeeeecCC
Q psy8714         458 --NESIPDFKPGDLIPIQSVKMVERKTTP  484 (562)
Q Consensus       458 --~~~Lp~l~~G~~~~~~~~~i~e~~TkP  484 (562)
                        +..||.|++|+.+.+.++.+.+++|+|
T Consensus       232 ~~~~~LP~l~~g~~~~~~~~~~~e~~TkP  260 (260)
T d1cy9a_         232 DEDRILPAVNKGDALTLVELTPAQHFTKP  260 (260)
T ss_dssp             --CCCCCCCCTTCEEEEEEEEEEEEECCC
T ss_pred             cccccCCCCCCCCEEEEeeeeecCCcCCC
Confidence              567999999999999999999999998

>d1vdda_ e.49.1.1 (A:) Recombination protein RecR {Deinococcus radiodurans [TaxId: 1299]}

class: Multi-domain proteins (alpha and beta)
fold: Recombination protein RecR
superfamily: Recombination protein RecR
family: Recombination protein RecR
domain: Recombination protein RecR
species: Deinococcus radiodurans [TaxId: 1299]

Probab=93.04  E-value=0.021  Score=51.84  Aligned_cols=59  Identities=8%  Similarity=0.036  Sum_probs=47.1

Q ss_pred             cccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEE--------ecccCHHHHHHHHHhCCCCh
Q psy8714         104 AKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRAR--------FSAITDKDIKAAMWNLVKPN  167 (562)
Q Consensus       104 ~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~--------~sslt~~~I~~A~~nl~~~~  167 (562)
                      +++..+||+||+|.-|||.-+..|.+.++..     +.+|.|+=        +.-++...+.+||++-+..+
T Consensus       131 ~~~~~EiIlA~~~t~EGe~Ta~yi~~~l~~~-----~ikitrlA~GiP~G~~ley~D~~TL~~Al~~R~~i~  197 (199)
T d1vdda_         131 VGQGMEVILATGTTVEGDATALYLQRLLEPL-----GAAISRIAYGVPVGGSLEYTDEVTLGRALTGRQTVS  197 (199)
T ss_dssp             CCTTCEEEECCCSSHHHHHHHHHHHHHHTTS-----SCEEEECCBCBCTTCCGGGSCHHHHHHHHHTCEEEE
T ss_pred             ccCCcEEEEEecCCcchHHHHHHHHHHhhhc-----CceEEeecccCCCCcchhhcCHHHHHHHHHcCccCC
Confidence            4556799999999999999999999999642     56788873        34578889999998866443

>d1mw9x_ e.10.1.1 (X:) DNA topoisomerase I, 67K N-terminal domain {Escherichia coli [TaxId: 562]}

class: Multi-domain proteins (alpha and beta)
fold: Prokaryotic type I DNA topoisomerase
superfamily: Prokaryotic type I DNA topoisomerase
family: Prokaryotic type I DNA topoisomerase
domain: DNA topoisomerase I, 67K N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=87.31  E-value=0.38  Score=50.48  Aligned_cols=109  Identities=17%  Similarity=0.282  Sum_probs=69.6

Q ss_pred             hhhhhhhhhhhccc-CcceEEEEEEEeeCCeEEEEEee----cc--cccC--HHHH-HHHHHHhhhcCceEEEEEEccee
Q psy8714         219 GFCVERHDKIRTFK-PEPYWLLDLTLNLNGVAVSVTWS----RG--HIFD--KSTC-NVFFKAVEKEKHVTVVDVQSSTK  288 (562)
Q Consensus       219 ~lIv~Re~eI~~F~-p~~y~~i~~~~~~~~~~~~~~~~----~~--~~~~--~~~a-~~~~~~~~~~~~~~V~~v~~~~~  288 (562)
                      .||+.|..+  +|- |..|....+.+..++..|.+...    .|  .++.  .... +..+-.+.....+.+.+++.+++
T Consensus       391 ~LI~rrfla--s~~~~a~~~~t~~~~~~~~~~F~a~g~~~~~~Gw~~v~~~~~~~~~~~~lp~l~~g~~~~~~~~~~~e~  468 (591)
T d1mw9x_         391 QLIWRQFVA--CQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKGDEDRILPAVNKGDALTLVELTPAQH  468 (591)
T ss_dssp             HHHHHHHHH--HTSCCEEEEEEEEEEEETTEEEEEEEEEEEECGGGGGSCCC----CCCCCCCCCTTCEEEEEEEEEEEE
T ss_pred             HHHHHHHHH--hccCCeEEEEEEEEeeecCcEEEEEEEEEEecCceEEecccccccccccCCCcCCCCEEEEEEEEEEEe
Confidence            456666554  454 44555666777777777766431    11  1111  1111 11222233334567888999999


Q ss_pred             eccCCCCCCHHHHHHHHHhhCCCC-HHHHHHHHHHhHhcCcee
Q psy8714         289 SKTKPQALNTVELMRVASSGLGMG-PHHAMQIAERLYTQGYVS  330 (562)
Q Consensus       289 ~~~pP~pf~l~~Lq~~a~~~~g~s-~~~tl~iaQ~LYE~glIS  330 (562)
                      .+.||.+|+-++|.+.+- ..|+. |+-=..|.+.|.++|||.
T Consensus       469 ~TkPP~~yTeatLi~~ME-~~GIGTpATra~iIe~L~~R~Yi~  510 (591)
T d1mw9x_         469 FTKPPARFSEASLVKELE-KRGIGRPSTYASIISTIQDRGYVR  510 (591)
T ss_dssp             ECCCCCCCCHHHHHHHHH-HTTCCCTTTHHHHHHHHHHTTSEE
T ss_pred             ecCCCCCCCHHHHHHHHH-hCCCCCcccHHHHHHHHHhCCCEE
Confidence            999999999999999884 46776 555567789999999986

>d1q1ha_ a.4.5.41 (A:) Transcription factor E/IIe-alpha, N-terminal domain {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcription factor E/IIe-alpha, N-terminal domain
domain: Transcription factor E/IIe-alpha, N-terminal domain
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=86.56  E-value=0.21  Score=38.87  Aligned_cols=33  Identities=24%  Similarity=0.334  Sum_probs=29.1

Q ss_pred             HHHhhCCCCHHHHHHHHHHhHhcCceeecCCCC
Q psy8714         304 VASSGLGMGPHHAMQIAERLYTQGYVSYPRTET  336 (562)
Q Consensus       304 ~a~~~~g~s~~~tl~iaQ~LYE~glISYPRTds  336 (562)
                      +.++.+|+....+-++++.||++|+++|-|.-.
T Consensus        38 ~iA~~tgi~in~VRk~Ly~L~~~~L~~y~R~kd   70 (88)
T d1q1ha_          38 EIANQLNIKVNDVRKKLNLLEEQGFVSYRKTRD   70 (88)
T ss_dssp             HHHHTTTSCHHHHHHHHHHHHHHTSCEEEEEC-
T ss_pred             HHHHHhCCcHHHHHHHHHHHHhCCceEEEEeec
Confidence            356789999999999999999999999998654

>d1r7ja_ a.4.5.49 (A:) Sso10a (SSO10449) {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Archaeal DNA-binding protein
domain: Sso10a (SSO10449)
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=83.17  E-value=0.41  Score=37.40  Aligned_cols=36  Identities=17%  Similarity=0.216  Sum_probs=30.9

Q ss_pred             hHHHHHhhcCCeEEEcCCCeeecchhHHHHHHhhhcc
Q psy8714         509 PVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKI  545 (562)
Q Consensus       509 a~iI~~L~~r~Yi~~~~~k~l~~T~~G~~li~~l~~~  545 (562)
                      ..+++.|.+.|+|+. .++.+..|++|+.+.+.++.+
T Consensus        36 ~kyl~~L~~~GLI~~-~~~~Y~iT~kG~~~L~~~~~~   71 (90)
T d1r7ja_          36 GRYIKMLMDLEIIRQ-EGKQYMLTKKGEELLEDIRKF   71 (90)
T ss_dssp             HHHHHHHHHTTSEEE-ETTEEEECHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCeee-cCCEEEECccHHHHHHHHHHH
Confidence            459999999999986 567999999999999887653

>d1jgsa_ a.4.5.28 (A:) Multiple antibiotic resistance repressor, MarR {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Multiple antibiotic resistance repressor, MarR
species: Escherichia coli [TaxId: 562]

Probab=81.60  E-value=0.54  Score=39.16  Aligned_cols=51  Identities=12%  Similarity=0.184  Sum_probs=38.9

Q ss_pred             CCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEc----CC--CeeecchhHHHHHHhh
Q psy8714         488 LTESELISLMEKHGIGTDASIPVHINNICQRNYVTVT----SG--RRLVPTSLGIVLVHGY  542 (562)
Q Consensus       488 ~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~----~~--k~l~~T~~G~~li~~l  542 (562)
                      .|..+|-..|   || +++|-+.+|+.|.++|||.+.    ++  +.+.+|+.|+.+++.+
T Consensus        49 ~t~~ela~~~---~i-~~~~vs~~v~~L~~~glv~r~~~~~D~R~~~i~lT~~G~~~~~~~  105 (138)
T d1jgsa_          49 ITPVELKKVL---SV-DLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTGGAAICEQC  105 (138)
T ss_dssp             BCHHHHHHHH---TC-CHHHHHHHHHHHHHTTSEEEEECTTCSSCEEEEECHHHHHHHHHH
T ss_pred             CCHHHHHHHH---CC-CHhHHHHHHHHHhhCCCEEEeeccCCCCeeEEEECHHHHHHHHHH
Confidence            3556666665   34 788888999999999999862    12  3699999999988553

>d2bv6a1 a.4.5.28 (A:5-140) Transcriptional regulator MgrA {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator MgrA
species: Staphylococcus aureus [TaxId: 1280]

Probab=80.11  E-value=0.7  Score=38.25  Aligned_cols=50  Identities=4%  Similarity=0.064  Sum_probs=36.8

Q ss_pred             CHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEc----CC--CeeecchhHHHHHHhh
Q psy8714         489 TESELISLMEKHGIGTDASIPVHINNICQRNYVTVT----SG--RRLVPTSLGIVLVHGY  542 (562)
Q Consensus       489 Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~----~~--k~l~~T~~G~~li~~l  542 (562)
                      |.++|...|   |+- ++|-..+|++|.++|||.+.    ++  ..+.+|++|+.+++.+
T Consensus        50 t~~~la~~l---~~~-~~~~s~~l~~L~~~Gli~r~~~~~D~R~~~l~lT~~G~~~~~~~  105 (136)
T d2bv6a1          50 NVKKVVTEL---ALD-TGTVSPLLKRMEQVDLIKRERSEVDQREVFIHLTDKSETIRPEL  105 (136)
T ss_dssp             EHHHHHHHT---TCC-TTTHHHHHHHHHHTTSEEEEECSSSTTCEEEEECHHHHHHHHHH
T ss_pred             CHHHHHHHH---CCC-HhHHHHHHHHHHHCCCEEEeecCCcccchhhccCHHHHHHHHHH
Confidence            444555444   554 57788999999999999862    12  3589999999988654